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Archive: Cell Trends Too

CellTrends

This thread presents evidence to back up my opinion that the apparent complexity and sophistication of cellular mechanisms is growing with time and additional research.
My source is http://www.creationsafaris.com/crev200610.htm

New Role for Ubiquitous ATP Molecule: Pain Trigger 10/26/2000
Nature’s Feature of the Week reports on a new role for the amazing ATP molecule. “ATP – adenosine triphosphate – is to the body what oil is to the industrialized world. Produced in virtually every cell of every living thing, it is the primary power source for reactions as diverse as muscle contraction, protein synthesis and heat generation. Now new research confirms a very different role for ATP – as a trigger for pain receptors.”

Multiple functions for parts is an example of design efficiency and elegance. The 1997 Nobel prize winners in chemistry found that ATP in living things from single-celled organisms to man is generated by a complex three-phase proton motor. One biologist was heard to say that if these mechanisms stopped working, you would be dead before you hit the ground.

Cells Do Their Own Triage 01/30/2001
According to an article in this week's Science News (Vol 159 p. 54, 01/27/01), specialized proteins perform emergency first aid and morgue duty. Proteins dubbed "chaperones" are able to recognize badly-folded proteins and fix them. Another protein acts as a coroner and breaks apart proteins that are beyond repair.

Proteins cannot perform their duties if they are not folded properly. The folding gives the protein chain (a string of amino acids) its three-dimensional structure, which is essential to its function. This kind of intricate molecular origami is accomplished partly by the affinities of parts of the molecule for each other due to the specific order of amino acids (that is why the sequence of amino acids cannot tolerate much error), and partly with the assistance of helper enzymes. But mistakes happen. How does the cell recognize an error?

Gentlemen, Start Your Engines 01/23/2001
The Proceedings of the National Academy of Sciences describe more findings about our amazing molecular motor, ATP Synthase (a complex enzyme that won its elucidators the 1997 Nobel Prize). Your body has trillions of these tiny motors in the mitochondria of cells. Each motor is 200,000 times smaller than a pinhead, and rotates at 6000 RPM, generating three ATP molecules per revolution (if these motors stopped, you would be dead before you hit the floor). The motor is reversible and can be used as a proton pump. ATP is the energy currency of every living thing. An active person can generate his/her body weight in ATP in a day’s time. Today’s report describes more details of the rotor and stator, and contains color diagrams of these amazing molecular machines on which all life, even bacteria, depends.

“Dead” Plant Cells Regulate Their Water Intake 01/26/2001
Xylem isn’t just deadwood, according to a new study in the journal Science. The woody cells respond to changes in salinity and mineral content, and can regulate the speed at which water rises in the stem. How a tree can pump water up hundreds of feet is still a feat not thoroughly understood, and now this study casts new light on a function of cells thought to be inert. Reported in ScienceNOW 29 December 2000: 2

New Function Discovered for Human Brain Glia Cells 01/29/2001
Glia cells, which make up 90% of the human brain, are not as functionless as earlier believed, according to a story in the journal ScienceNOW 26 January 2001: 1 .They play an important role in determining how many connections the neurons can make with each other.

Newly-Published Human Genome Reveals Mysteries 02/12/2001
The Los Angeles Times has two stories about surprising discoveries being made now that the fully-mapped human genome is being published (on Charles Darwin’s birthday, by the way). The first is that differences between humans are small. The other is that our functional genome is only about twice that of a fly or roundworm and only a hundred more genes than a mouse. Apparently the rest of our genome contains a great deal of transposed material from other species, which may explain much of so-called “junk DNA.” Nature is providing a new online news and information service on the human genome, the Genome Gateway, and also has several gene-related stories on its daily Nature Science Update page. Not to be outdone, Science has a special issue devoted to the human genome, free to all users.

Protein Folding Regulated by Quality Control 02/20/2001
The upcoming Feb. 29 issue of the Philosophical Transactions of the Royal Society is devoted to protein folding and disease. As we reported earlier, it has been discovered that cells have chaperones that supervise and proofread the folding of amino acid chains of which proteins are composed. In the preface to this edition of the Transactions, the editors speak of the quality control processes of the cell, stating that “Failure to satisfy the quality control process, particularly by proteins resulting from genetic mutations, is associated with a wide range of diseases including cystic fibrosis and diabetes.” (Normally, misfolded proteins are “rigorously excluded” from the cell.) “And because it is so strongly linked to fundamental cellular activities, any aberrations in the folding process will lead to malfunctioning of the organism involved, and hence to disease.”

Cells are much, much more than building blocks or aggregates of organic molecules: they have central storage of information and detailed processes for carrying out instructions and correcting mistakes. Without these, life could not exist. Considering how precise the quality controls must still be maintained in this cursed, mutating world, Dr. Joseph Henson used to say, “The surprising thing is not that we get sick, but that we are ever well.”

Biological Motor Has Tight Specifications 02/21/2001
Scientific American has an article about dynein, a protein essential to cell division, which the article describes as a protein motor composed of 12 parts. Researchers have found that “in order to function properly, dynein’s components must have a certain form and must fit together in a particular way. Problems with even a single component, it turns out, can have disastrous effects.” This line of research may help lead to anticancer treatments by disarming dynein in cancer cells. Click here for the Ohio University press release with further details.

Genetic Potential Increases 02/22/2001
New findings provide further evidence that the old “one gene – one enzyme” paradigm is incorrect. Researchers at Johns Hopkins have found that two genes in combination can make multiple proteins through a process called trans-splicing. Apparently messenger RNA can simultaneously read both halves of a DNA molecule in opposite directions and splice them together. This increases the protein-generating potential of the human genome, which was announced earlier this week to have fewer genes (around 30,000) than expected.
This means the DNA stores vastly more information than could be stored on one strand, the other being just a template. It is just one of many marvels sure to come out of our ongoing investigation of the genetic code. The whole story of transcription by messenger RNA to transfer RNA to protein, accompanied by a host of specialized enzymes, is dazzlingly complex and exquisite in its precision and speed.

Life From Nonlife Made Simple 03/05/2001
“Missing Links Made Simple” is the voilà! title from an article in today’s Nature, summarizing an experiment announced in the Proceedings of the National Academy of Sciences. The vexing problem of the origin of proteins, specifically how to get amino acids to link up with peptide bonds, has evaded naturalistic solution for decades. But researchers from Scripps Institute have found that short segments of Transfer RNA (tRNA) assisted by puromycin molecules carrying amino acids can form peptide bonds without the assistance of ribosomes, provided some imidazole is around to help. They claim that this process also encodes some information into the chain: the tRNA bound to the puromycin better when their sequences matched. “The evolution of this control over protein manufacture holds the key to the emergence of the living from the non-living worlds.”

If-Then Algorithm Found in Brain Wiring 03/08/2001
Scientists at UC San Francisco have found a wiring algorithm for nerve cells in developing embryos. Nerve cells, or axons, use neurotransmitters to guide their growing ends toward their proper connection sites: attractants call out “this way” and repellants say “keep out.” But what if both an attractant and a repellant appear at the same time? They found that the repellant wins the draw, and the repellant receptor then physically binds to the attractant receptor to deactivate it.

Update 03/12/2001: Scientific American summarizes a report in the journal Science about how growing tips of nerve cells send signals. Scientists found that they use short bursts of calcium, lasting only 300 milliseconds, to scout out their surroundings as they grow toward their destinations.

Biochemist Claims Ancestor to ATP Enzymes Found 03/09/2001
A Purdue biology professor claims that acetate kinase resembles the structure and function of other metabolizing enzymes in bacteria and archaea, and may be the common ancestor of these enzymes that utilize ATP for energy.… Notice that even though the these enzymes have an outward resemblance (a similar fold), they have entirely different amino acid sequences.

How Do Cilia Move in Concert? 03/12/2001
Cilia, the microscopic hair-like projections on some single-celled organisms such as Paramecium and in the human body such as the lining of the esophagus and digestive tract, have long puzzled biologists with their ability to beat in synchronized wave patterns. In the March 22 issue of the Biological Proceedings of the Royal Society, two Israeli scientists use 3D modelling to simulate how this motion is achieved and find that the viscosity of the surrounding medium influences the motion.

Update 03/14/2001: Nature has just published a paper … on the bacterial flagellum. The flagellum is now seen as a reversible helical propeller that allows the bacterium to switch between running and tumbling modes.

Natural Amplifier Found in Inner Ear 03/27/2001
A paper in the Proceedings of the National Academy of Sciences, summarized here in Scientific American, describes new findings about how ears work. A newly discovered “motor protein” named prestin acts as an amplifier. Found on the tips of the microscopic outer hair cells in the cochlea, it takes the electrical energy converted by the inner hair cells and converts it back into mechanical energy, thus amplifying the sound.

The pressure waves in the air that make up sound can be as low as 2 x 10-5 N/m2, yet the sensitivity of the eardrum, the ossicles, and the cochlea to these whispers of sound is astounding – the ear can handle intensities of a million million to one. The eardrum’s microscopic vibrations are amplified by the bones of the middle ear twentyfold as they transmit from air to fluid in the inner ear, where further amplification takes place. This article provides just one more detail on the process. Like all other proteins, prestin is made up of hundreds of amino acids, all left-handed, that are arranged in a precise sequence to allow it to perform its job as an amplifier

Eye Does Image Processing 03/28/2001
A scientist at U C Berkeley claims that stacks of cells in the retina process the image received by the photoreceptors, then sends 12 parallel data sets to the brain that contain only the bare essentials of the image. “What the eye sends to the brain are mere outlines of the visual world, sketchy impressions that make our vivid visual experience all the more amazing,” the report claims.

Last edited by bob b; October 15th, 2006 at 11:25 AM.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Protein Sequencing Makes Winning Lottery Look Easy 04/04/2001
In the world of protein molecules, it is possible for two totally different proteins to perform the same function, much like you can open a jar with your hand or with a wrench. But while discussing this fact, Nature Science Update today makes some surprising admissions about the improbability of getting a usable protein by chance. In an article about bioengineering, author John Whitfield states: “If you wanted to make a working protein, but didn’t know where to start, how many rolls of the biochemical dice would it take to get lucky? One hundred billion, say Anthony Keefe and Jack Szostak, of the Massachusetts General Hospital in Boston, who’ve tried it to hunt out proteins to do a predetermined job from a vast number of random genes.
“These sort of odds make buying a lottery ticket seem like a sound investment. They suggest, says Ronald Breaker, a molecular biologist at Yale University, New Haven, Connecticut, that you’d have to strain a sizeable quantity of primordial soup before you found something that evolution could get its teeth into.”

Common Ancestor of Plant Carbon-Fixing Found? 04/16/2001
A report published in the Proceedings of the National Academy of Sciences claims that a protein similar to the one that fixes carbon from CO2 has been found in green sulfur bacteria. The protein appears to perform some other functions in the bacterium as well.

Biological Motor Caught on Film 04/18/2001
The Japanese have succeeded in capturing images of ATP Synthase, the world’s tiniest motor, according to Nature Science Update. This incredibly small proton motor rotates at thousands of RPM and cranks out ATP molecules, the energy currency for all living things. Your body has uncounted trillions of these motors spinning right now, providing the energy for every heartbeat, muscle contraction and chemical process. The Japanese images of the motors show unprecedented detail and, for the first time, actually show the little motor turning. “We couldn’t ever build a motor that small - but nature has,” remarks one scientist. On April 24, Science reported on this story with a picture of how they photographed one of nature’s most “splendid machines.”

Eye Neurons See Their Way to the Brain 04/20/2001
Through a series of clever experiments on frogs and fruit flies, researchers at the University of Utah have identified some of the genes responsible for the development of eyes and their nerve connections to the brain. Without the genes, the neurons seem to get lost and go in circles, but with the gene, the neurons “see” their way to the proper connection point in the brain.

Article 04/17/2001: Tom Bethell, writing for the American Spectator an article entitled “The Road to Nowhere” (reproduced on the Discovery Institute website, claims “The genome isn’t a code, and we can”t read it.” He reports how the human genome is far more complex than earlier claimed, because the old one-gene one-protein hypothesis appears to be incorrect; a gene can code for several tens of proteins. The article contains statements by Dr. David Baltimore, James Watson and other prominent DNA scientists to the effect that it may be many decades before we understand how the human genome works and what it says; predictions that our computers could crack the code appear overly optimistic.

Cell News 04/16/2001: Two articles from the Journal of Cell Biology on wonders in the cell, summarized in EurekAlert: (1) A story about control mechanisms involved in cell division, and (2) A story about how yeast cells are able to keep their nuclei in the center. There is also a story summarized in Science Now describing how plants can sense the cold and adjust their processes to keep from freezing. And on April 18, (4) EurekAlert published a summary of a study that explores how white blood cells are able to find their way to infected areas.

Our Humanness: Gene Sequence, Gene Activity, or Something More? 04/24/2001
Both Nature and Scientific American summarized today the flavor of discussions from the Human Genome Meeting that just concluded in Edinburgh; apparently, it is not the sequence of our genes, but the amount of activity in the way they are expressed, that makes us human. Gene sequences between humans and chimpanzees differ by as little as 1.3%. Something else is clearly involved in making us what we are. A German scientist found that although the sequences of genes in apes and people are similar, their expression in the brain is poles apart. The genomes of all mammals are so similar that “it’s hard to understand how they can produce such different animals, says Sue Povey, who works on human gene mapping at University College London in England. What drives similar genes to have such divergent degrees of expression, if it is not DNA? No one knows. On April 27, ABC News posted a story about the relation of the genome to the “proteome,” the protein library, with some illustrations of how proteins work.

Did Crystal Power Make Proteins Southpaws? 05/01/2001
NASA astrobiologists have published a paper in the Proceedings of the National Academy of Sciences on experimental evidence that calcite crystals and other minerals might selectively concentrate left- and right-handed amino acids (click here for summaries in Scientific American or Nature. NASA’s Astrobiology Site also has a lay-audience version of the story.) All living organisms incorporate only left-handed amino acids into their protein chains; the choice of left or right appears to be arbitrary, but life depends on 100% of one hand or the other. In these experiments, the team achieved yields of just under 10% preference for one hand. This is significant for origin of life scenarios, the paper concludes, because minerals could have not only concentrated one hand over the other but also arranged them into chains.

Proteins Are Vastly More Complicated than Previously Realized 05/03/2001
That’s the title of a report today on NewsWise.com SciNews. Biochemists are realizing that proteins are not just static 3-D shapes; they are subject to dynamic forces of stretching, pushing and pulling that affect their function. Protein folding has been likened to a kind of delicate origami, but researchers at the University of Washington take the analogy further: “Imagine trying to fold a delicate origami crane from silk paper - while you’re in a wind tunnel. In fact, imagine trying to fold the origami in a wind tunnel while countless other hands are also pulling at the paper. And yet, that’s comparable in complexity to what the hundreds of thousands of cells and proteins are doing in your body right now.” Dr. Viola Vogel is in the forefront of this new field that studies how protein functions change under dynamic stresses. “We are very excited about this because we believe a new field is being born: non-equilibrium protein structure-function analysis. It’s very exciting to think about how nature regulates and controls function. We went from viewing the cell as a bag full of proteins a decade ago to a view of the cell as a dynamic place where proteins assemble and change under mechanical forces,” she says. An update summary 05/29/2001 in Scientific American claims that proteins are moving all the time, very fast, and that these motions affect their functions.

Astrobiologists Give Up on Primordial Soup, Look to Comets 05/21/2001
A feature story in Science News May 19, 2001 (pp. 317-319) deals with origin of life woes. In “Cosmic Chemistry Gets Creative,” Jessica Gorman rounds up the usual suspects (McKay, Chyba, Bada, et al) to put a positive spin on a desperate situation: the old Miller primordial soup theory appears dead, so they are looking to seeding earth with prebiotic chemicals via comets. Scientists are blasting material together to try to form building blocks of life in hypothetical comets, and see if they could survive the fiery plunge to earth.

Distributed Shipping Design Found in Nerve Cells 05/25/2001
Researchers at the Howard Hughes Medical Institute have found that dendrites, the long stems on neurons, have the ability to manufacture their own proteins. Erin M. Schuman, Institute investigator from CalTech, remarked on the economy and efficiency of this design: “It’s like the difference between centralized and distributed freight shipping,” she said. “With central shipping, you need a huge number of trucks that drive all over town, moving freight from a central factory. But with distributed shipping, you have multiple distribution centers that serve local populations, with far less transport involved.”

Cell Nucleus Surface More Complicated than Expected 06/14/2001
Researchers at North Carolina State University made an unexpected discovery: cell nuclear membranes are groovy. The surfaces of some plant cells were found to contain tunnels and grooves with complex channels used by RNA, enzymes and organelles to enter and exit the cell’s master control center. They found that parts of the endoplasmic reticulum (a system of folded channels) passes right into the center of the nucleus, and watched organelles moving along actin filaments in the grooves. Dr. Nina Allen, botanist at the university, said, “The implication of this discovery is that we need to look more closely at communications between the nucleus and the cytoplasm, and we need to understand why these grooves and tunnels are there.”

What they witnessed was a highly complex transportation system at work. Imagine a city with overlapping monorails shuttling cargo loads in all directions, with loading docks, signalling systems and security checks: this is what goes on in miniature inside the cell. The picture of the cell that is being slowly revealed to our instruments is one of bewildering complexity.

PNAS Explores How Cells Transport Freight 06/19/2001
The June 19 Proceedings of the National Academy of Sciences has a colloquium section devoted to molecular kinesis, a fancy term for the study of how cells ship their freight around, such as from nucleus to cytoplasm and back. Some common themes in the colloquium are: (1) Cells are much more complex than we previously thought; (2) There is still much we don’t know; (3) Any slip-ups in the machinery mean disease or death.

Bacteria Genes Evolved, Not Hopped, into Human Genome 06/25/2001
Evolutionists have come up with an explanation for 113 genes that were earlier reported to be candidates for horizontal gene transfer from bacteria to humans. They say that the genes have a common ancestor, but that some lines lost the gene. The explanation is published in Nature Science Update, which claims that “the gold standard for establishing whether horizontal gene transfer has occurred is drawing up evolutionary trees to trace a candidate gene’s inheritance.”

Cells Use Triple Fail-Safe Systems During Division 06/28/2001
During cell division, when millions of DNA base pairs are duplicating, a lot could go wrong and lead to runaway duplication – e.g., cancer. Now, scientists have found at least three mechanisms that drastically reduce the chance of failure. According to Scientific American. Joachim Li at the University of California, San Francisco, said, “We eventually demonstrated that not one or two but at least three distinct controls have to be turned off simultaneously for cells to start replicating again. This is unlikely to happen by accident, so this multilayered protection is virtually fail-safe. That’s what you want when there is no room for error.”

Last edited by bob b; October 15th, 2006 at 11:22 AM.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Duke Biologists Deny Validity of Molecular Classification 07/02/2001
Scientists at Duke University claim to have debunked the method of classifying mammals and other organisms based on mitochondrial DNA sequences. The molecular method claims the platypus is related to the kangaroo, for instance, and that widely disparate animals like hippos and whales had a common ancestor. The Duke scientists analyzed nuclear genes with computer software that supported the older common-sense classification used by paleontologists that groups animals based on morphology (outward structure and anatomical similarities). The article starts by saying, “Classifying kangaroos and platypuses together on the evolutionary family tree is as absurd as adding your neighbors to your own family ancestral line simply because they share your love of the opera, according to scientists at Duke University.”

Clones Express Genes Differently 07/06/2001
Why do so many cloned embryos die before birth? Why do the ones that survive have abnormalities? According to scientists at MIT reported by Scientific American News, it’s because clones express genes differently than the donor; i.e., even though the donor and the clone have identical DNA, they do not activate the same genes in the same way. Apparently there are “epigenetic” factors at work, influences other than the coded language of life. These include enzyme tags on genes that affect their expression. Embryonic stem cells with nuclei from donors can have different tags that cause them to develop in wildly different ways, producing chimeras (monsters), abnormally large offspring, or survivors that while appearing outwardly normal have hidden abnormalities that can lead to problems later.

Human Genome 07/10/2001: The BBC reports that some scientists dispute earlier estimates that the human genome only has 30,000 genes. Using different statistical techniques, they claim it has over twice as many: 70,000 or more.

Update 08/24/2001: A report in Nature puts the number at 42,000 but admits it could go higher than 50,000. One of the difficulties is the algorithms used to estimate the number of genes, and the lack of knowledge of function of various sequences.

Update 11/28/2001: According to EurekAlert, scientists at Cold Spring Harbor laboratories, Long Island NY, now have a computer program able to spot gene "on" switches and promoters. They think the number of human genes is now between 50,000 and 60,000.

See also the report in the Feb 22, 2002 issue of Science about discussion among members of the AAAS.

Plants Talk to Themselves in Email 07/13/2001
How does one part of a plant know that another part is under attack, or how do the roots know the weather is changing and affecting the leaves? According to Nature, plants have a busy system of email messages spreading the news. Scientists have discovered messenger RNA (mRNA) molecules travelling from cell to cell and onto their own little Internet (the phloem), that apparently let one part of the plant know what’s going on in another part.

25 Years of Study on DNA Copy and Repair Mechanisms Summarized 07/18/2001
The July 17 issue of the Proceedings of the National Academy of Sciences contains a long paper by two MIT biochemists on what we have learned so far in 25 years of study of enzymes that help copy and repair DNA: the DNA polymerases. Apparently these wonder molecules not only synthesize DNA but repair a number of different kinds of errors. The coordination of which polymerase is activated and tosses the baton to another is still poorly understood. Most of the work has been done on E. coli, a prokaryote (simpler one-celled organisms lacking a nucleus), but the situation is even more complex in the eukaryotes (all higher organisms), “where both the number of DNA polymerases and the level of complexity of the events are far greater.”

The authors seem truly amazed at the performance of these submicroscopic molecules. Some sample sentences:
• A common, defining feature of these DNA polymerases is a remarkable ability to replicate imperfect DNA templates . . .
• The recent discovery of additional eukaryotic DNA polymerases...further complicates the already daunting issue of understanding the control systems that govern which DNA polymerase gains access . . . .
• A growing body of evidence suggests that an important additional level of control results from DNA polymerases being "coached" as to their correct biological role through interactions with other proteins associated with the particular DNA substrate . . . .
• In addition to their roles in chromosomal DNA replication, DNA polymerases participate in numerous DNA repair pathways, including double-strand break repair, mismatch repair, base excision repair and nucleotide excision repair . . . .
• Elaborate regulatory controls and a sophisticated system of protein-protein contacts ensure that the...gene products carry out their appropriate biological roles. However, as is so often the case in science, the discoveries of today are posing even more challenging questions for tomorrow.

Frankenstein Bacteria Jumpstart Evolution With Lightning 08/01/2001
According to Nature Science Update, researchers in France simulated lightning in soil with spark discharges and observed bacteria incorporating plasmids (DNA rings) into their genomes. They conjecture that this method of horizontal gene transfer might be instrumental in evolution.

Quotable Quote 08/02/01: “The simplest living cell is so complex that supercomputer models may never simulate its behavior perfectly. But even imperfect models could shake the foundations of biology.” – W. Wayt Gibbs, “Cybernetic Cells,” Scientific American (August 2001), p. 53.

Master On-Off Switch for Genes Found: A Second Genetic Code? 08/10/2001
Researchers at the University of Virginia have been studying a type of protein structure called chromatin that surrounds DNA, and believe it acts as a switch to turn genes off or on. If so, this is another source of information, like a second genome, that helps regulate DNA genes. Dr. C. David Allis, a biochemist, states: “We believe that what is telling the cell to make those choices is an overall code that may significantly extend the information potential of the genetic DNA code. For some time, we have known that there is more to our genetic blueprint than DNA itself. We are excited that we are beginning to decipher a new code, what is referred to as an epigenetic code.” The story was reported by SciNews.

Motor and Clutch Proteins Identified for Cellular Highways 08/17/2001
Did you know that cells have their own interstate highway system, with actin filaments serving as streets and microtubules serving as freeways? That motors send their cargo zipping down the lanes? EurekAlert reports that biologists at the University of Illinois, publishing in Science, believe they have identified the clutch that puts the motor in neutral or clicks it into gear. While studying pigment organelle movement in animals that can change color, like chameleons, they think they have uncovered a universal system for moving parts around the cell. The clutch is a complex molecule named calcium/calmodulin-dependent protein kinase II (CaMKII); it works to engage or disengage a motor protein they had earlier identified as myosin-V.

Electricity Propels Cell Cargo 08/21/2001
Cells need to move stuff around through microtubules, little subway tunnels, and build proteins on assembly lines called ribosomes. How do they attract the trucks to the cargo bay and move them along the track? One factor appears to be static electricity. Scientists found ways to calculate the electrostatic potential of microtubules and ribosomes, and found that they have complex quilted patterns of positive and negative charges, with a net negative charge that helps attract the ingredients and propel them along, according to a paper published online in the Proceedings of the National Academy of Sciences.

The paper is technical, but has some nice illustrations of microtubules in cross section. It shows how the little tunnels are not simple structures like hoses, but elaborate, precise arrangements of molecules as intricately crocheted as a quilt. The main ribosome components have 88,000 to 95,000 atoms apiece, arranged to create the proper electrostatic potential.

Of Centromeres and Telomeres 10/05/2001
Two cell biology reports are revealing that “mere” parts of DNA are vital. A news release in Nature announced that a university team in Cleveland, Ohio has sequenced the centromere of the human genome. These are the junction points that join the two strands of chromosomes. They consist of long repetitive sequences of genetic letters. Though no one understands how they work at this point, they parcel out equal shares of chromosomes during cell division. Flaws in the centromeres are implicated in many cancers.

In a second news item, a paper in the journal Cell discusses the role of telomeres in cell death and cancer. Telomeres are the “end caps” on DNA strands that prevent them from unraveling; at each cell division, the length of the telomere is reduced by one unit. Researchers found that the shortest telomere determines when the cell signals itself to die, not the average telomere length. Scientific American comments that cells with short telomeres act as if the DNA strand has broken, and receive a signal to “arrest or die as a protection against chromosome rearrangement and cancer.” When the telomere-repair tool, telomerase, is present, it lengthens the telomere just enough to function. Runaway telomere lengthening appears to be a characteristic of some cancers. A related paper published online in the Proceedings of the National Academy of Sciences demonstrates that “telomere dysfunction triggers extensive DNA fragmentation and evolution of complex chromosome abnormalities in human malignant tumors.”

Virus Motor Packs DNA Under High Pressure 10/18/2001
University of California at Berkeley scientists have measured the force with which viruses stuff their DNA into protein bottles called capsids. A little molecular motor at the lid of the bottle is able to pack the coiled DNA with 60 piconewtons of pressure. On a human scale, that is ten times the pressure in a champagne bottle. The team is now studying whether the pressure is used to inject the DNA into the host bacterial cell, and whether the packing motor rotates as do some other molecular motors studied, such as the bacterial flagellum.

Thermodynamics of Cellular “Steam Engines” Described 10/22/2001
Three Japanese scientists have analyzed the thermodynamics of molecular motors in living cells in a new paper in the Biological Proceedings of the Royal Society. They compare the thermodynamic properties of macroscopic steam engines vs. the microscopic motors like dynein and myosin-V involved in cellular transport and cell division. They describe how these “remarkable microscopic engines” are able to perform a biased random walk (like a ratchet), even though buffeted by Brownian (thermal) motion, and perform useful work. The same equations shown here for linear molecular motors should be applicable to rotary motors like ATP synthase.

Tiny RNAs: A Whole New World of Regulators Discovered 10/26/2001
Cell biologists have uncovered a whole new class of regulators that control development and gene expression: micro-RNAs, or miRNAs. These short sequences of genetic material (usually around 10-30 nucleotides, much smaller than genes) that had “almost escaped detection until now,” may number in the hundreds or thousands in the cells of all living things. They work not by coding for proteins, but by latching onto messenger RNAs, that are en route to the protein assembly plants, and inhibiting them until the right time, thus acting as switches or timing controls. But the range of possible functions is just now beginning to be explored. One geneticist comments, “Each miRNA is probably matched to one or more other genes whose expression it controls. Their potential importance to control development or physiology is really enormous. If there are hundreds of these in humans and each has two or three targets that it regulates, then there could be many hundreds of genes whose activity is being regulated this way.” Three reports on miRNAs are in the Oct 26 issue of Science. See also this summary in SciNews.

How Plants Stand Up 10/26/2001
Plants are able to stand erect because of their rigid cell walls. Scientists have known that cell walls contained a complex carbohydrate called RG-II, but didn’t know its function. Now, scientists at the University of Georgia have figured out that RG-II forms a fishnet-like arrangement held together by boron atoms that, along with cellulose, gives the cell wall rigidity something like reinforced concrete. This carbohydrate, one of the most complex in nature and used by all plants, requires a host of enzymes to manufacture:

“RG-II has been known as an obscure, structurally weird polysaccharide that plants make,” said Malcolm O’Neill, senior research associate at UGA’s CCRC. “But we had no idea why plants went to all the effort to make it. There are 50 to 60 enzymes involved, 12 different sugars and 22 different linkages. There’s even one sugar that’s actually not been found anywhere else.”

They observed that mutants lacking a crucial side chain on the carbohydrate, or lacking boron, end up as dwarfs. The plants returned to normal by the addition of the missing ingredients.

Cell’s Golgi Body Recycles Itself Continuously 11/12/2001
The Golgi apparatus, a maze of channels near the nucleus of a cell whose function was mysterious a few decades ago, is gradually revealing its secrets. Scientists at Virginia Tech and Heidelberg have found that the proteins making up the apparatus are constantly being renewed, according to EurekAlert. One of the scientists describes what the Golgi body does:

"The Golgi apparatus is a complex organelle. It is involved in the processing of proteins destined for either secretion or for the outer surface of the cell. Traditionally, scientists have looked on the Golgi apparatus as a fixed structure that processed proteins in an assembly-line fashion.

The organelle is a cup-shaped arrangement of layers of flattened sac-like membranes that’s located in a characteristic place near the cell’s nucleus. Proteins are processed through the layers of the Golgi apparatus, with enzymes in each layer causing modifications as the proteins proceed through the layers, finally to be shuttled into vesicles that take them to the cell’s surface.

Vesicles are bubble-like containers that bud from the Golgi apparatus and transport proteins to the cell's surface membrane. The vesicles themselves are made of proteins, which are absorbed by the surface membrane when they have completed their mission. Proteins are delivered to the Golgi apparatus for processing in vesicles that bud from the endoplasmic reticulum. Therefore . . . “there is a constant flow of materials from the endoplasmic reticulum through the Golgi and to the cell’s outer surface."

The new “central finding” about the Golgi body is that it is “not a fixed structure, but that every component of it is recycled through the endoplasmic reticulum. This recycling allows the replacement of frayed proteins, acting as a kind of quality control to ensure the structure can perform its function.”

Update 01/11/2001: More on the Golgi apparatus in Science, “the central protein sorting station of the cell,” especially how it creates protein vesicles for transport: a very complicated series of steps involving enzymes and lipids working together.

How Did Cell Nucleus Evolve? Nobody Knows 11/19/2001
In a new Explore feature, Scientific American investigates current thinking about how eukaryotic cells evolved a nucleus, and concludes that no theory currently explains all the facts. Some think that early cells developed a symbiotic relationship with bacteria or archaea, but the nucleus has unique features that are not present in either assumed progenitor. Every theory has serious objections. One biochemist admits, “We really probably don’t have any idea what happened. It does seem like, whatever happened, it was probably very complicated and not very sensible.”

How the Ameba Crawls 11/22/2001
Yale scientists have gained new insight into how cells move, reports EurekAlert. They’ve revealed the 3-D structure of seven proteins called the Arp2/3 complex that assembles actin proteins into filaments, which push the front of the cell forward. A similar process (actin polymerization) is involved in white blood cells moving to the site of an infection, and in neurons branching out into the million miles (more or less) of axons and dendrites in the human brain. Thomas Pollard of Yale, co-author of the paper in Science, explains how it works. Chemicals in the environment send messages to the Arp2/3 complex, which in turn cause it to orient the cell and move in a particular direction. He says, “Actin and Arp2/3 complex work like a peculiar motor in a car to make the cell move forward. Rather than turning wheels, the filaments grow like branches of a bush to push the cell forward. Arp2/3 complex is very ancient, having evolved in primitive cells well over one billion years ago.”

Your Non-Essential Genes Protect You 11/23/2001
Scientists at the National Institutes of Health have been scanning through 3,760 non-essential genes in yeast and finding them not so useless after all. So far, they have found 107 that apparently protect from radiation and toxins in the environment. Non-essential genes are ones the organism can live without – grow and develop into maturity without apparent harm. When danger lurks, however, these genes are switched on and provide protection. Since these genes in yeast and mammals are similar, they expect similar protection is afforded humans by these “non-essential” genes. (Source: EurekAlert.)

Sunburn Repair Protein Found 11/26/2001
A protein named interleukin-12, a type of cytokine, has been found to be effective in reversing damage caused by the sun’s ultraviolet light. According to Nature Science Update, it appears to work by activating the DNA to edit out mistakes: “The protein appears to stimulate a cellular editing system that snips damaged pieces of DNA out of the sequence,” the report states. Cells with interleukin-12 were actually able to reverse sunburn damage. If IL-12 is this effective, other cytokines may also be involved in DNA repair. “This is probably the tip of the iceberg,” says Kenneth Kraemer of the National Institutes of Health, commenting on the paper in Nature Cell Biology.

Last edited by bob b; October 15th, 2006 at 11:18 AM.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

“Motor proteins are tiny vehicles that move molecular cargoes around inside cells. These minute cellular machines come in three broad families, the kinesins, the myosins and the dyneins. There are over 250 kinesin-like proteins, and they are involved in processes as diverse as the movement of chromosomes and the dynamics of cell membranes. They all have a similar catalytic portion, known as the motor domain, but beyond this they are astonishingly varied - in their location within cells, their structural organization, and the movement they generate.”

She spends time especially on the “Ferrari” of these motor vehicles, a kinesin from the fungus Neurospora crassa, that can move along its microtubule tracks at 2.5 microns per second, five times faster than other similar kinesins (if this molecule were the size of a car, it would top 1200 mph). Describing three possible means of achieving such speeds, she suggests ways microbiologists might learn more about “these splendid molecular machines.”

Two other papers (1), (2) in the same issue discuss ATPase or ATP synthase, the molecular motor of exquisite precision and function discussed earlier in Creation-Evolution Headlines. The second describes how it is involved in helping stomata (openings) in a plant leaf open and close to exchange gases. Apparently ATPase creates an electrical potential that works with other proteins that are responsive to blue light.

These motor vehicles (80 times smaller than a wavelength of light) and the microtubule tracks they run on have been likened to a nanotrain or intracellular railroad system in the cell.

Mature Muscle Stem Cells Can Make Blood 12/11/2001
Nature Science Update is reporting that mature muscle cells in mice have stem cells that can migrate to form blood cells, then come back and make more muscle, an “amazing thing,” according to the University of Pittsburgh researchers who reported to the American Society for Cell Biology. They weren’t even looking for stem cells in the muscle tissue. Helen Blau at Stanford says, “It shows that cells can go in many different directions given the right environment.” She believes the traditional view that stem cells permanently lose their ability to produce other cell types is changing. Others argue that research on embryonic stem cells should continue.

Cells Squeeze Out Their Dead 12/13/2001
Cells die, and if left in place in tissues, they would shrivel, rot and leave a hole. Something must be done, and the cellular machinery is built to handle every contingency. At the American Society for Cell Biology meeting this week, the process was described by London biologists, reports Science Now. Early in its death throes, the dying cell sends out a warning to neighboring cells, who produce extra motor proteins actin and myosin. These go into action retracting the healthy cells around it into a contractile ring, as if saying Heave ho on cue, squeezing the dead cell out like toothpaste, then reforming the intact tissue. The scientists switched the proteins on and off in skin epithelial tissue to test their hypothesis.

Wonders of the Water Gate 12/20/2001
The Dec. 20 issue of Nature has a detailed description, with diagrams, of one of the water gates inside you (and all living things): AQP1, one of the aquaporins, the superfamily of complex proteins in cell membranes that transport water into the cell interior. There are ten families of these water channels. In this paper, Berkeley scientists achieve the highest yet resolution (2.2 Angstroms) of the structure of AQP1, and show it to be a highly-organized, specifically shaped and sized pore with inner and outer vestibules, between which is a constriction region with a “selectivity filter” that lets water in but not anything else.

DNA Damage Response Team to the Rescue 01/04/2002
Americans proudly hail the firefighters and cops that go to work when terror strikes, but did you know your body has an even more heroic team that flies into action when DNA gets damaged? It’s called the DDR - DNA Damage Response team. The hearty band of specialized enzymes can handle any contingency: broken strands, loose ends, typos, kinks, twists and numerous other emergencies. During complex operations like duplication and translation, the DDR team has its P&P (policies and procedures) down pat, including checkpoints and feedback mechanisms to ensure repairs are made quickly, or that irreparable damage triggers the appropriate salvage and disposal operations.

Writing in the Jan 4 issue of Science, a team of seven geneticists, biochemists and biologists have determined that no less than 23 separate genes code for the DDR (and there are probably more). In addition, they noted an “extraordinary level of conservation of molecular mechanisms in DDR pathways” in all living things, from the worms they studied to man. Many kinds of cancer can be traced to defects or mutations in these genes, that leave the cell like a city without a fire department.

Ancient Cells Proofread Better 01/08/2002
Four biochemists from Stratagene in California, writing in the Proceedings of the National Academy of Sciences, have identified a complex “proofreading” enzyme that improves DNA copying accuracy up to 100-fold. The enzyme is composed of multiple protein chains and can survive high temperatures (around 200oF). Although with this proofreading enzyme copying is slowed down (550 nucleotides per minute instead of 2,800 without the proofreading), the fidelity is greatly increased. It apparently works by breaking down a product called dUTP produced by other construction pathways. dUTP can poison a replicating DNA chain by substituting uracil. All living things contain a suite of proofreading enzymes, including members of this family of enzymes (dUTPases) that “read ahead” and find dUTP to cut it out of the growing DNA strand. But this one is not only highly effective, it works at high temperatures. The surprise is that this bulky, complex enzyme was found in a single-celled organism of the kingdom Archaea (“ancient ones”) which includes bacteria that thrive in hot springs.

Note: Several other papers on DNA proofreading can be found in the January 8 preprints of PNAS, each equally interesting and amazing, such as this paper by biochemists at the University of Washington on nucleotide excision repair (NER), the ability of enzymes to repair breaks in DNA caused by ultraviolet light damage. (They studied this in yeast)

How Life Defends Against Harmful Mutations 01/31/2002
Different populations have different ways of defending themselves against the destructive effects of harmful mutations, say David C. Krakauer of the Sante Fe Institute and Joshua B. Plotkin of Princeton, in a paper “Redundancy, antiredundancy, and the robustness of genomes” in the Jan 29 Proceedings of the National Academy of Sciences. Although presuming genetic mutations are a source of evolutionary novelty, they explain that damage must be guarded against.

The authors propose that small populations of large organisms (like mammals) use redundancy to maintain fitness: i.e., copies of genes and backup systems. But large populations of small organisms, like bacteria, appear to employ antiredundancy strategies: i.e., they are hypersensitive to mutation, but employ methods of removing harmful mutants:

“Assuming a cost of redundancy, we find that large populations will evolve antiredundant mechanisms for removing mutants and thereby bolster the robustness of wild-type genomes; whereas small populations will evolve redundancy to ensure that all individuals have a high chance of survival. We propose that antiredundancy is as important for developmental robustness as redundancy, and is an essential mechanism for ensuring tissue-level stability in complex multicellular organisms. We suggest that antiredundancy deserves greater attention in relation to cancer, mitochondrial disease, and virus infection.”

The authors propose a mathematical model for explaining the dynamics of redundancy and antiredundancy in differing populations. Populations exhibiting redundancy have hilly fitness landscapes with steep, narrow peaks. Antiredundant populations have a flat fitness landscape with small peaks, forming a “quasispecies” of mutants with similar fitness.

Rotating Gate in the Cell Membrane a “Beautiful Design” 02/12/2002
Another gateway into the cell has been explored, and it’s a beauty, say the three biochemists who describe it in the Proceedings of the National Academy of Sciences Feb 12 online preprint. This one is called KcsA, a potassium ion channel that is critically important for nerve impulses in humans, but also is used by bacteria. KcsA is one of many membrane proteins that are subjects of intense scrutiny by biochemists. It is so effective, it can let in 10,000 potassium (K+) ions for every unwanted sodium ion (Na+), even though sodium ions are smaller but have same charge.
How the KcsA channel does this was a surprise. Apparently, four helical rod-shaped parts rotate clockwise in such a way as to keep parts of the gate rigid while allowing other parts to flex. To picture this in a simplified way, visualize four chopsticks hanging vertically, forming a square looking from the top down. Each stick has a pivot point about 1/3 of the way down, allowing it to rock. The bottom ends of the sticks are bundled together in the shape of an inverted teepee, in such a way that as each stick pivots, the bottoms trace out a circle. Moving in concert, they cause a rotary motion that allows the potassium ions funnelling into the stiff upper part, the “selectivity filter” wide berth as they exit into the interior of the cell. The selectivity filter, like a one-way ID-checking turnstile, attracts positive potassium ions but keeps unwanted molecules out.
The authors explain how only a clockwise rotation allows the gate to work. They did not state the rotation rate of the gate, but it must be phenomenal; the throughput of KcsA is an astonishing 100 million ions per second, very near the diffusion limit. The authors apparently could not help expressing a little awe in their otherwise straightforward scientific paper; they used the word “design” twice: “The interplay of the two pivot points is a beautiful design by nature for solving the gating problem of KcsA,” and “The swinging rotational motion of TM2 helices with two pivot regions is an exquisite design by nature to ensure an effective gating of KcsA without having to loosen up the structural integrity near the intracellular side of channel in the open state.”

Presto! Prestin Wins the Gold in Molecular Motor Race 02/21/2002
A “new type of molecular motor, which is likely to be of great interest to molecular cell biologists” has been discovered. Named prestin, this protein motor, made up of 744 amino acid units, is a speed demon, ferrying negative ions across cell membranes in millionths of a second. It appears to function as part of the mechanical amplifier in the cochlea, helping the ear to achieve its “remarkable sensitivity and frequency selectivity.” Nature Molecular Biology Reviews describes the unique features of this biological machine:

"Prestin is a new type of biological motor. It is entirely different from the well-known and much-studied classical cellular motors in that its function is not based on enzymatic processes, but on direct voltage-to-displacement conversion. The action of prestin is also orders of magnitude faster than that of any other cellular motor protein, as it functions at microsecond rates."

Prestin has an external voltage sensor that causes it to respond. Its action apparently mediates changes in length of the outer hair cells of the cochlea, greatly amplifying the responsiveness of vibrations reaching the inner ear. The illustration in the article shows how the cochlear amplifier works to provide variable, automatic, amplitude-dependent response. The “gain” on low-level signals can be 1000-fold, but intense signals are not amplified. This allows the brain to hear very faint signals but not get saturated by loud ones.

Update 02/26/2002: A paper in the Proceedings of the National Academy of Sciences describes prestin further and finds that it is dependent on regulation by thyroid hormone.

Sound begins as miniscule pressure waves in the air. These are first channeled by the outer ear into a tunnel, where they set up vibrations in the eardrum, then are transmitted mechanically through three lever-action bones to the inner ear, then are amplified by hair cells in the cochlea (each responding to its own characteristic frequency), which open and close ion channels that send electrical pulses down the auditory nerves. The brain, then, sorts out all this information to determine frequency, amplitude, direction, and meaning.

Delays in hearing could be dangerous. The rapid response of prestin and all the other components of our amazing sound system helps us to hear in real time. Scientists are just now beginning to understand the details of operation of the long-mysterious cochlea, with its keyboard-like rows of inner hair cells and outer hair cells that expand and contract in perpendicular directions.

Bewildering Complexity – RNA Editing 02/21/2002
The Feb 22 issue of Cell contains a paper by Alabama biochemist Stephen J. Hajduk entitled “Editing Machines: The Complexities of Trypanosome RNA Editing.” RNA editing is critical to the accurate building of molecular machines like ATP synthase vital to cells. The author asks, “How many proteins does it take to edit an RNA?”

"Recent studies, using conventional protein purification, homology modeling, and mass spectrometric analysis, have focused on identifying the components of editing complexes. This is an important yet somewhat bewildering exercise since at least a dozen proteins have been identified that putatively contribute to RNA editing in trypanosomes."

He describes how these proteins form editing complexes, and how RNA strands pass through several iterations of editors on their way to the protein assembly plant. In the last section, “Increasing complexities and unresolved issues,“ Hajduk states: “As we begin to understand the composition of the editing machinery, new complexities emerge.”

Introns Found in Primitive Eukaryote 02/26/2002
Science Now reports that introns have been found in Giardia, a primitive eukaryotic single-celled organism. Sometimes considered “junk DNA,” introns are pieces of genetic code that do not code for proteins, that have to be cut out of the strand by genetic scissors called spliceosomes before transcription can begin. Introns were thought to have evolved later in the eukaryotic line, but here they were, scissors and all, in an early “primitive” eukaryote. The original paper is in the Feb 19 Proceedings of the National Academy of Sciences.

Protein Folding an Olympic Event 02/27/2002
A news release from the University of Pennsylvania puts biological molecules into the Winter Olympics:

"It’s a long-simmering debate in the world of physical chemistry: Does the folding of proteins into biologically active shapes better resemble a luge run - fast, linear and predictable - or the more freeform trajectories of a ski slope? New research from the University of Pennsylvania offers the strongest evidence yet that proteins shimmy into their characteristic shapes not via a single, unyielding route but by paths as individualistic as those followed by skiers coursing from a mountain summit down to the base lodge."

The researchers, who published in this week’s Proceedings of the National Academy of Sciences, found a great deal of variety in the paths and rates of folding. Only when a protein is folded correctly can it perform its function. Misfolded proteins are the cause of many serious diseases. The team explains that there are chaperones on hand to fix errors:

In the skiing analogy, chaperones could be thought of as rescue helicopters that return wayward skiers to the summit so they can try to make their way down the mountain again,” said [Feng] Gai, an assistant professor of chemistry at Penn.

Protein folding is fiendishly intricate, yet crucial to the chemistry of life - so much so that a small army of biologists and chemists has devoted itself to better understanding the process.

Another article in another source describes just how fiendishly intricate the process is. The March 12 issue of PC Magazine has a feature section on Technology in America. Alan Cohen describes how supercomputers, after showing their skill in deciphering the human genome, are trying to tackle the puzzle of protein folding:

"Problems like protein folding, where the number of possible shapes for the average-size protein is greater than the number of atoms in the universe, are far more complex. Thus, such problems require “a tighter, faster, parallel machine, where the processors of each work in conjunction with the others,” says Professor [David A.] Bader [director of the High Performance Computer Lab at the University of New Mexico]."

"... Advances like these require intense computation, and as impressive as the clusters that sequenced the genome are, they’re not enough for this new phase.

IBM’s Blue Gene project, which will be able to perform 1 quadrillion operations per second, sets out to tackle protein folding. IBM scientists estimate that calculating the folding process of even a very small protein on today’s most powerful computer would take 300 years. Even Blue Gene, once completed in 2005, will take a year to crunch the numbers."

Last edited by bob b; October 15th, 2006 at 11:14 AM.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Batteries, Chaperones, Translators: Wonders of the Cell Continue to Dazzle 03/08/2002
Recent techniques have allowed scientists to peer into the cell at 1.6-nanometer resolution. What has appeared in sharp detail is a veritable factory of living machines that can manufacture things, charge batteries, edit code and much more. The March 8 issue of Science has several papers that explore more the complex goings-on inside our cells, and even the cells of the lowly bacterium E. coli:

• Battery Rechargers: Three biochemists have described how some anaerobic bacteria recharge their batteries. To get work done, all organisms have to use electricity. They do this by pushing charges the way they don’t want to go (against the energy gradient), creating an electromotive force (in this case, PMF or proton motive force). The authors examined the proton pump in the membrane of E. coli, and found that it is a complex of very complicated protein molecules shaped somewhat like a mushroom. It effectively passes proteins down a 90-angstrom channel somewhat like an electric wire, using a series of chemical reactions called a redox loop.

• Assembly Plant: The cell is a crowded place. Newly manufactured proteins, if not protected before folded into their proper shape, can turn into harmful gunk. Not to worry; a family of chaperone proteins is at their service to whisk the proteins to safe barrel-shaped havens where they can fold in peace. Two German biochemists have examined the process from newly-synthesized chain to folded protein:

“To become functionally active, newly synthesized protein chains must fold to unique three-dimensional structures. How this is accomplished remains a fundamental problem in biology. Although it is firmly established from refolding experiments in vitro that the native fold of a protein is encoded in its amino acid sequence, protein folding inside cells is not generally a spontaneous process. Evidence accumulated over the last decade indicates that many newly synthesized proteins require a complex cellular machinery of molecular chaperones and the input of metabolic energy to reach their native states efficiently.”

They describe some of the bad things that can happen: aggregation or clumping, which might be implicated in Alzheimer’s disease and Huntington’s disease, among many other problems. The paper describes a staggering array of complex chaperone molecules and procedures that work together to prevent trouble under a wide variety of conditions.

• Editing Room: Two Greek biochemists from Crete peer into the process of transcribing a gene of DNA into messenger RNA, which then travels to the ribosome to build a protein. It’s not a simple job. The DNA is bundled tightly into balls of chromatin and nucleosomes, preventing the editing apparatus from getting to it. Again, not to worry: there is a squad of chromatin-unscramblers to unlock the precious code and let the translator, RNA-polymerase II, scan the code and build the messenger RNA. Think of scrolls locked in a library of ancient manuscripts that need to be translated into English. These scrolls contain the instructions for building machines. You need someone with a key to let you in, then you need a way to safely unroll the scroll to the right spot. These steps must precede the translation and manufacturing processes. In this paper, the scientists found that two squads are needed. A pre-initiation complex (PIC) gets the unrolling machinery ready before the door is unlocked. A chromatin-remodeling squad unlocks the door. The unlocking is actually more like unscrambling tightly-wound strands so that the PIC can get to it, before the translator can do its work.

Scientists Coax Molecules to Self-Assemble 03/12/2002
Nanotechnology, the use of molecules to build machines, is a hot topic these days. Makers of these invisibly-small robots are imitating nature, taking their cues from living systems. In the March 12 preprints of the Proceedings of the National Academy of Sciences, there are two papers describing how scientists have gotten molecules to self-assemble into structures. One team got star-shaped building blocks to assemble into tubes: “Entropically driven self-assembly of multichannel rosette nanotubes.”. In the same issue of PNAS, another team describes how molecular-size machines and motors might be built from various molecules in “Controlled disassembling of self-assembling systems: Toward artificial molecular-level devices and machines”.

Gates of the Cell Open to Awe-Struck Eyes 03/12/2002
The cover story of the March 9 Science News Vol 161:10, pp 152-154 is about ion channels, the complex gates that attract and channel electrically-charged atoms into the cell (see our Jan 17 and Mar 7 headlines on this topic). The article has color diagrams of the complex proteins that make up the channels and describes how they function: the KcsA potassium channel, for instance, “can shuttle up to 100 million potassium ions across a cell membrane in a single second while keeping out similarly charged sodium ions, whose smaller size would seem to make the passage easier.” (Sidelight: Nature Science Update reports that scientists have engineered a synthetic chloride channel, imitating nature.) The importance of ion channels is emphasized:

“Literally every single thought or action involves these channels. After all, among their duties is regulation of the electrical excitability that nerve cells use to communicate and that muscles exploit to contract.”

Roderick MacKinnon and other researchers who first revealed their intricate structure were surprised that lowly bacteria had fully-formed ion channels:

“There was something even more surprising. No one had previously reported voltage-gated ion channels in a microbe. Jellyfish were the simplest creatures known to possess such channels. It was generally thought that microbes, which lack muscles and nervous systems, don’t need the high-speed reactions that voltage-gated ion channels permit.”

“This changes the whole evolutionary picture of [ion] channels,” says Clapham. “It means that bacteria, the most primitive life forms, have what was thought to be a very specialized channel.”

The descriptions of these channels and their fast-acting voltage-regulated gates borders on awe at times. MacKinnon, though pleased at the possibility of medical advancements now that ion channels are becoming better understood, “admits that he’s motivated more by the thrill of understanding these remarkable proteins. ‘I just wonder how nature does things,’ he says. ‘How did nature make an electrical signal go from my brain to my toes so fast? The more you learn about what the ion channels have to do to make that signal, the more incredible it seems.’”

DNA Computer Demonstrated 03/14/2002
Meet the DNA computer: humans using biological molecules to perform non-biological calculations. Dr. Leonard Adelman of USC got DNA to work a difficult combinatorial problem, says a news release at Jet Propulsion Laboratory which partly funded the research. The advantage of DNA molecules is that they can operate in a massively-parallel fashion, unlike serial processing done by our familiar electronic computers. They are also very energy efficient and capable of storing vast quantities of information. Adelman exults:

“We’ve shown by these computations that biological molecules can be used for distinctly non-biological purposes. They are miraculous little machines. They store energy and information, they cut, paste and copy. They were built by 3 billion years of evolution, and we’re just beginning to tap their potential to serve non-biological purposes. Nature has given us an incredible toolbox, and we’re starting to explore what we might build.”

Adelman’s report is published in the March 15 Science.

Did Proteins Self-Organize? 03/19/2002
The Proceedings of the National Academy of Sciences for March 19 published a supplement on “Self-organized complexity in the physical, biological, and social sciences.” In the only paper of the colloquium that might bear on evolution, Hans Frauenfelder of Los Alamos labs considers Proteins: Paradigms of Complexity. He describes complexity: “A system can be called complex if it can assume a large number of states or conformations and if it can carry information.” Proteins and DNA, he explains, can assume so many possible combinations that they make astronomical numbers seem small by comparison: yet proteins and DNA carry information, “Hence proteins, and in general biological systems, are complex.” He describes the complex conformations of amino acid chains, the energy landscape of protein interactions, and the many functions they perform. Then he concludes with this enigmatic statement :

“This brief sketch should make it clear that proteins are truly complex systems and that the complexity can be described through the energy landscape. The complexity has arisen through evolution. The structure and function of proteins are coded in the DNA. Within the living system, proteins are part of a complex proteins network, and the complex interactions in the network may control the actual function. Can this be called self-organized?”

Biologists Drowning in Complexity 03/21/2002
So admits an opinion page, “Pursuing Arrogant Simplicities,” in the March 21 Nature, stating :

“Generating vast sets of data from stressed cells in order to determine patterns of gene expression is an immense step forward. But beware the false impression that we are close to understanding how networks of genes regulate one another’s expression, and generate phenotypes such as cellular development and behaviour. Even the true scale of most genetic networks is unknown. And biologists know that genes are just one aspect of control: protein switches and molecular signalling networks are still a largely uncatalogued universe. ...
.... Even after one absorbs a thousand or more pages of text, one would still be unlikely to have a feel for the variability and complexity of even the simplest microbe.”

The comments were made in regard to universities that are building multi-disciplinary centers to model biology, warning them not to take life too simplistically. While the editors encourage a search for simple, breakthrough hypotheses to model such things as genetic networks, the editors ask, “But what if, as some biologists suggest, there may be no possible model simpler than life itself?”

Factory Recall: How the Cell Deals with Assembly Errors 03/22/2002
From DNA to protein – the process of transcription and translation, in which a messenger RNA (mRNA) reads the DNA template and ferries the information to a ribosome, where transfer RNAs (tRNA) assemble amino acids into protein chains, is an elaborate process coordinated with dozens of enzymes, signals and molecular machines. The mRNA is supposed to come with a “termination codon” a specific series of nucleotides that tells the ribosome the chain is complete. But what is the ribosome to do when the mRNA is missing the termination codon, or has it in the wrong place? If it releases a misfit protein, the results could be disastrous. Not to worry: the cell has control procedures to recognize the error and dismantle the misfit protein before it gets into circulation. Two papers in the March 22 issue of Science explain new findings about the factory recall system, termed nonsense-mediated messenger RNA decay and nonstop messenger RNA decay. Several mechanisms are involved. Though complicated, they resemble human assembly lines with inspectors that stamp bad parts defective, so that downstream workers know to send them to the recycle bin (an exosome or proteasome) instead of the shipping room. Other mechanisms resemble instructions from a high-tech spy novel: something like “if the messenger arrives more than 22 minutes late or is lacking his security clearance emblem, activate his self-destruct mechanism.” In her perspective summary, Lynne E. Maquat begins, “Prokaryotic and eukaryotic cells have evolved remarkable quality assurance mechanisms at virtually every step of gene expression.” Maquat also has a summary of the processes in the March 19 issue of Current Biology.

Cell’s Motors– Are Really Motors 03/26/2002
James Marden and Lee Allen from Penn State, writing in the March 26 PNAS, “Molecules, muscles, and machines: Universal performance characteristics of motors” have graphed the net force vs mass of motors from molecular size to rocket engines. They found essentially no difference between biological motors like ATP synthase, the bacterial flagellum, dynein and other nano-scale molecular machines and man-made motors:

“Animal- and human-made motors vary widely in size and shape, are constructed of vastly different materials, use different mechanisms, and produce an enormous range of mass-specific power. Despite these differences, there is remarkable consistency in the maximum net force produced by broad classes of animal- and human-made motors.”

In addition, they compared “flying birds, bats, and insects, swimming fish, various taxa of running animals, piston engines, electric motors, and all types of jets” and found them to all fall on the same line of force per mass, except in a few cases where viscosity of the medium was a factor. “Remarkably,” they state, “this finding indicates that most of the motors used by humans and animals for transportation have a common upper limit of mass-specific net force output that is independent of materials and mechanisms.” They are not sure if living things have achieved a theoretical upper limit of performance per unit mass, but conclude: “In the meantime, we perhaps can only marvel that millions of years of natural selection on animals and a few centuries of experimentation with machines have resulted in an empirical and evolutionary solution to the problem; ...”

As is typical each week in the Proceedings of the National Academy of Sciences, the same issue has a plethora of additional research papers about wonders of living cells: for example,

• How cells protect against UV damage
• How water pores help secretory vesicles swell up like water balloons
• How taste buds detect sweetness
• How cells protect their proteins from oxidative damage
• How the cell maintains the integrity of its mitochondrial DNA
• Another essential protein that regulates cell division

Another Protein Chaperone Found 03/28/2002
German scientists writing in the March 28 Nature have described another “protease-chaperone machine” in cells that is widely conserved in living things. Named DegP, this molecular machine has two functions: if it cannot refold a badly-folded protein, it dismantles it. Its functions appear to be heat sensitive. The six-sided cluster of protein chains forms a barrel-shaped cavity, with “a construction reminiscent of a compactor.” Customers are guided by tentacle-like “gatekeepers” into the machine, and the door is closed. If the customer just needs cleaning to refold, the lint is scraped off and the molecule is ejected to refold; otherwise, it is compacted and destroyed. The machine is apparently versatile enough to handle many different kinds of proteins.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Cell Assembly Line Workers Tethered Together 04/04/2002
A paper by two Harvard biochemists in the April 4 Nature explores new findings that the molecular machines that perform gene expression are all tied together (coupled) in assembly-line fashion, so that one process hands off to the next instead of waiting for the next machine to show up by chance:

“Recent studies lead to the view that, in contrast to a simple linear assembly line, a complex and extensively coupled network has evolved to coordinate the activities of the gene expression machines. The extensive coupling is consistent with a model in which the machines are tethered to each other to form “gene expression factories” that maximize the efficiency and specificity of each step in gene expression.”

In describing the elaborate processes that read and translate DNA, the paper uses the words machine or machinery 53 times, and factory or factories 10 times. And there’s more: “Superimposed on this pathway is an RNA surveillance system that eliminates aberrantly processed or mutant pre-mRNAs and mRNAs” – i.e., a quality control subsystem.

Why Cancer Is Rare 04/04/2002
Anyone who has been diagnosed with cancer, or had a loved one with it, knows what a frightening and unwelcome surprise it is. But according to Robert Weinberg, cancer researcher at the Whitehead Institute for Biomedical Research, the surprise is that our bodies are usually so successful in preventing it: “There are so many things that need to go wrong, so it is not surprising that, in a lifetime, cancer is actually rare.” Most cancers are caused by mutations, and very few cancers are caused by a single mutation. Mutations tend to accumulate as the cancer progresses; that is why early treatment is usually successful. Weinberg’s comment appears in a status report on cancer research by Alison Abbott in the April 4 Nature.

Two Unlike Proteins Do the Same Job 04/06/2002
Two unlike organisms, yeast and a protozoan, have proteins that bind to telomeres; these proteins are required for chromosome end protection and telomere replication. They look alike and do the same job, but are very different in amino acid sequence, reports a paper in the April 5 Science. The authors believe this “indicates that mechanisms of telomeric end protection are widely conserved throughout evolution.”

In another paper in the same issue, British biochemists have found a chromatin protein that is conserved in archaea, bacteria, and eukaryotes (including people). The protein Sir2, in combination with Alba, is important for repressing expression of genes not needed at the time. They conclude that “this partnership may have been highly conserved throughout evolution.”

Bacteria Are Champion Proofreaders 04/10/2002
A team of Australian biochemists has examined the structure of just one of the “proofreading enzymes” in E. coli bacteria in unprecedented detail, and formulated a hypothesis for how it works. That it does work, and works extremely well, is described in the introduction to their paper published in the April issue of Structure:

“Fidelity of DNA replication is determined by three processes: base selection by a DNA polymerase, editing of polymerase errors by an associated 3'-5' exonuclease, and postreplicative mismatch repair. In Escherichia coli, these processes contribute to duplication of the genome by the replicative DNA polymerase III (Pol III) holoenzyme with error frequency ~10-10 per base pair replicated.”

In other words, with its proofreading machinery, the bacterium makes a error once in 10 billion DNA letters.

First Cell Not Salt-Tolerant 04/15/2002
Charles Apel of UC Santa Cruz has found that the first cell could not have formed in salt water, so it must have formed in fresh, reports Academic Press and the NASA Astrobiology Institute.

“This is a wake-up call,” says mineralogist Robert Hazen of the Carnegie Institution of Washington in Washington, D.C. “We’ve assumed that life formed in the ocean, but encapsulation in freshwater bodies on land appears more likely.” Geologist L. Paul Knauth of Arizona State University in Tempe adds that Earth’s early oceans were up to twice as salty as they are today–making it even more difficult for viable cells to arise.

Astrobiologists had assumed lipid molecules would self-organize into vesicles, but apparently salt makes them fall apart. Apel’s findings were delivered at last week’s Astrobiology Conference, and will be reported in an upcoming issue of Astrobiology Journal.

Cell Water Channels Continue to Amaze 04/18/2002
If you enjoyed our December 20 story about aquaporins, the water gates of the cell, you’ll want to read this update posted by the University of Illinois with a cool animation of how the complex channel (made up of more than 100,000 atoms) allows a water molecule through in a billionth of a second, but keeps smaller protons out. Summarizing their paper in the April 19 Science, they explain:

“Aquaporins, a class of proteins, form transmembrane channels found in cell walls. Plants have 35 different proteins of this type. Mammals, including humans, have 10, with many of them in the kidney, brain and lens of the eye.”

When working correctly, said Klaus Schulten, the Swanlund Professor of Physics at the UI, the transport of water between plant cells lets flowers bloom and leaves stand sturdily, for example. In mammals, the machinery processes water efficiently to help maintain optimum health.

They go on to describe the problems that broken channels can cause: diabetes, cataracts, and breakdown of other organs…. A single aquaporin can process a billion water molecules per second without letting a single interloper through.

Evolution of an Enzyme Explained by Lateral Gene Transfer 04/29/2002
In the April 30 issue of Current Biology, a team of Canadian scientists claims to have found a relationship in an enzyme (ATP Sulfurylase) between archaea, bacteria and eukaryotes. They propose that lateral gene transfer (LGT) is the mechanism that spread this capability from one group to the other, and may be more important than mutation during redundancy (MDR) as a mechanism of evolution. If so, this puts a new twist on protein evolution: “As with the MDR model, it will be important to determine how functionally identical duplicates can escape from frequent silencing mutations until one of the duplicates acquires rare advantageous mutations. In any case ... the prevalence of LGT among prokaryotes and the ‘quantum’ leaps over sequence space it permits (in contrast to point mutation) suggests it could play a more important role in the evolution of gene function than previously recognized.”

Another DNA-Mending Protein Discovered 05/14/2002
Scientific American reports on a research paper that identified a protein named ATR as able to mend DNA damaged by ultraviolet light. The researchers explain, “ATR appears to act as a switch that starts the repair process and also stops cells from proliferating while they are being repaired.”

DNA Has Its Own Immune System: RNA 05/17/2002
The May 17 issue of Science has a special Viewpoint feature about the RNA library, or RNome (the RNA counterpart of the genome). We all know about DNA and proteins; RNA was long thought to be just the messenger/translator between the two. Scientists have increasingly found RNA molecules, however, to perform many crucial functions including signalling and expressing genes.

• Gary Riddihough introduces the new concept of the RNome and its multi-faceted role in many vital functions, such as protecting DNA from invasion.

• Gisela Storz describes an “expanding universe” of non-coding RNAs, including micro-RNAs (sequences of 20-22 bases), with a multitude of functions that we are just beginning to understand.

• Phillip Zamore says that RNA “reflect an elaborate cellular apparatus that eliminates abundant but defective messenger RNAs and defends against molecular parasites such as transposons and viruses.”

• Paul Ahlquist discusses how RNA can silence genes, which makes it a central player in gene expression.

• A team of scientists at Rockefeller University has elucidated the core structure of RNA polymerase at high resolution. RNA polymerase is a chief molecular machine involved in transcription of DNA. It makes a copy of a gene from a DNA molecule that can be ferried by messenger RNA to a ribosome, where transfer RNA assembles the amino acids based on the coded sequence into a protein machine. The researchers show RNA polymerase to be a complex system with multiple roles and moving parts, assisted by a suite of other protein machines. They say it is “conserved in structure and function among all cellular organisms,” from bacteria to man.

Proteins Climb Mountains 05/20/2002
Scientists at Caltech have found that proteins climb an energy mountain to get home. Nature Science Update describes how a protein chain begins as a string of amino acids, but must go through a complicated folding process that it calls “one of biology’s fundamental mysteries.” The scientists measured the “energy landscape” in the folding process. To get to its “native fold,” in which it is properly folded and functional, it must climb an energy mountain and settle in just the right valley on the other side. On the way, there are several pitfalls that the protein must avoid or else it becomes a useless tangle. Their research is published in the Journal of the American Chemical Society.

Membrane Channels Are Doorways to Health – or Death 05/29/2002
The latest issue of Neuron, May 30 has an essay about membrane channels and their importance. The authors of “Channels Gone Bad” begin:

“Channels regulate ion flow across membranes and are an essential component of cell function. Indeed, nearly all cell membranes contain ion channels, proteins with diverse roles, and sometimes highly complex behaviors. Channels are activated and inactivated by many signals and their function regulated by countless processes. Yet, beware of the aberrant channel. Channels that open when they shouldn’t, channels that do not open very well or at all, channels that stay open too long, misplaced channels, lack of channels, too many channels; all these scenarios can have disastrous consequences.”

They describe some of the horrible consequences of mistakes in the genes that code for these complex proteins: cancer, numerous types of disease, and death.

Published the same day, the May 30 Nature has a report on how ion channels open and close their gates, and features two more papers on this subject by the pioneer in this field, Roderick MacKinnon of the Howard Hughes Medical Institute: the crystal structure and gating mechanisms and conformational changes of potassium ion channels. The papers contain detailed pictorial models of how the channels and their selectivity filters attract and transmit the correct molecules rapidly and accurately, but repel interlopers.

DNA Translation Machinery Is the Major Cell Building Project 05/31/2002
“The ribosomal RNA [rRNA] genes encode the enzymatic scaffold of the ribosome and thereby perform perhaps the most basic of all housekeeping functions. However, recent data suggests that they might also control important aspects of cell behavior.” Thus begins a minireview in the May 31 issue of Cell, which says that one of the biggest, if not the ultimate, cellular subsystem is preparing and controlling the machinery to translate DNA into proteins:

“An actively cycling eukaryotic cell expends between 35% and 60% of its total nuclear transcription effort in making the 18S, 5.8S, and 28S ribosomal RNAs (rRNA) (Paule, 1998 , and references therein). The 5S rRNA and the small nucleolar RNAs required for ribosome biogenesis, account for another 10% to 20%. Thus, the assembly of the translational machinery occupies around 80% of nuclear transcription in yeast, while in the proliferating mammalian cell as much as 50% is dedicated to this goal. Even relatively small changes in this commitment are likely to have extensive repercussions on the cell’s economy, limiting proliferation rates and perhaps even cell fate. ... Though little is known of the changes that occur in vivo, one would suspect that, given the longevity of ribosomes and the highly variable proliferation rates of different somatic cell types, rRNA transcription rates must be regulated over a wide range if neither a ribosome deficit nor an overproduction is to occur.”

The minireview by Tom Moss and Victor Stefanovsky, “At the Center of Eukaryotic Life,” goes on to describe many functions of ribosomal RNA, including regulatory functions previously unknown. rRNA molecules appear to silence some genes, a mystery that may be explained by having backup copies available in case damage occurs to the highly active rRNA genes. They conclude, “Recent work argues that the rRNA genes are not simply bystanders in the decisions on cell fate. Understanding the regulatory network surrounding the rRNA genes is then an essential part of understanding cell growth regulation. It may even turn out that the housekeeper is in fact keeping the house.”

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Cell’s DNA Translation Machinery Revealed in Unprecedented Detail 06/13/2002
Japanese scientists publishing in the June 13 issue of Nature have revealed the molecular structure of the RNA polymerase holoenzyme, including its initiation factor, at 2.3 angstrom resolution (an angstrom is one ten billionth of a meter). This enzyme is one of the most important molecular machines in the cell; “The DNA-dependent RNA polymerase (RNAP) is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living organisms.” It builds all the RNA molecules: messenger RNA, transfer RNA, ribosomal RNA, and others. Moreover, the machine consists of five subunits that “are evolutionarily conserved in sequence, structure and function from bacteria to humans.”

The color models show a complex structure shaped somewhat like a lobster claw. It doesn’t work until the initiator named sigma (with four subunits itself), like a key, turns it on and attaches it to a promoter on the DNA molecule. Then it ‘melts’ the DNA at that point and unwinds the section of DNA to be transcribed, and releases the promoter. At that point, the machine undergoes a significant change in shape, and crawls along the strand, attaching RNA subunits into a chain. Apparently, two precisely-placed magnesium ions at the active site are essential for this catalytic activity. During the operation, the DNA appears to run through the cleft of the claw, the ‘active site’ somewhat like a zipper, with a series of alternating switch and trigger functions snapping together the ingredients and preparing the machine to move to the next step. To get a feel for how the machine works as it moves along, here is their description, jargon and all:

“Taken together, these structural data allow us to propose a possible mechanism for RNAP translocation during RNA synthesis. At the step of ‘relaxation’ (after translocation, before the next reaction), the template base at position i+1 is paired with the substrate nucleoside triphosphate (NTP), the bridge helix is in an all -helical conformation, the Arg 1,096 bridges the i and i+2 DNA phosphates, and the flexible trigger loop is distal (rather than proximal) to the bridge -helix. After phosphodiester bond formation, a signal induces the movement of the trigger loop towards the bridge -helix, pushing out the ‘switch’ residues. In their flipped-out conformation, the switch residues may engage the DNA phosphate at position i+1 and bring the bridge -helix under the DNA backbone towards the i+2 nucleotide. During this step, Arg 1,096 may also switch its interacting partner from DNA phosphates to the side chain of an acidic (polar) switch residue, thus simultaneously stabilizing the flipped-out conformation of the switch residues and facilitating the translocation of the enzyme.”

Cell Journal Marvels at Complexity, but Assumes Darwinism 06/17/2002
Book reviews in scientific journals allow scientists to back off from the detail and jargon of a specific paper and comment on the big picture. The June 14 issue of Cell is loaded with book reviews that are a study in contrasts. Details of cellular complexity and design are juxtaposed with simplistic evolutionary explanations. Some examples :

1. Standard Textbook: Patrick Williamson reviews the standard text Molecular Biology of the Cell (4th ed., 2002) and refers to the “dramatic complexity of the cytoplasm” that began to be revealed with electron microscopes in the 1950's. But in the end, he attributes it all “to natural selection in cobbling together solutions to pressing problems using the miscellaneous materials presented by gene duplication and mutation” ...

“In the past, we have sometimes spoken in deprecating tones of our scientific predecessors ‘stamp-collecting’ their way through the characterization of the phylogeny and life histories of the earth’s species. Now, the genome projects have presented us with new sets of stamps to collect, characterize, describe, and explain. Like our predecessors, we can’t usually reduce our insights into a few general principles because of the way organisms have evolved, but we can always anticipate growing satisfaction with the detail and clarity of our understanding of all the many instances we find.”

2. Mind Boggling Complexity: Max Gottesman, in a review of Genes & Signals by Ptashne and Gann (2001), slaps his head over the complexity of enzyme actions:

“Recall the days of yesteryear when, for biologists, enzymes were enzymes and didn’t need any help in finding their substrates. Alas, those simple times are long gone. Instead we are faced with the horrible realization that proteins rarely see their ligands without being led by the nose to them. So, for example, RNA polymerase once promptly landed on a promoter and revved up to transcribe a gene. It turns out, in fact, that for most promoters, RNA polymerase requires additional proteins just to find the site. And other proteins interfere with its attachment. The number of such auxiliary factors, especially in eukaryotes, is mind boggling ... The situation is scarcely better in signal transduction. A hormone can only relay its message to the nucleus via passage through a long series of proteins, most of which have to be spatially constrained to transmit the signal. Even the simple matter of removing a piece of unwanted RNA from a transcript involves the assembly of a dozen or so proteins and RNAs, probably in a configuration that is highly specific. The reason for all this is now quite clear. Transcription cannot be ubiquitous, but is regulated by factors that respond to cellular environment, cell type, phases of the growth cycle, etc. Similarly, transduced signals are not sprayed around the cell, but are channeled toward specific effectors, as determined by the special requirements of the cell at a particular point in time.”

3. Extreme Life: Thomas Cavalier-Smith takes a hard look at D.A. Wharton’s Life at the Limits: Organisms in Extreme Environments (2002). He likes the treatment of extremophiles and cryptobiotic organisms (those that can go into states of suspended animation), but criticizes his sparse treatment of the origin of life. He believes, contrary to the author, that eubacteria–flagella and all–are our ancestors, not archaebacteria:

“The origin of biomolecules is much easier to understand if it occurred in a heterogeneous environment with geothermal activity to condense polymers and numerous small cool pools subject to freezing and drying to stabilize and concentrate them. The breakthrough to the first organisms in which membranes, genes, and catalysts cooperated is also much easier to understand in a cool heterogeneous environment such as polar tide pools (Cavalier-Smith, J. Mol. Evol. 53, 555-595, 2001). It seems much more likely that early proto-organisms were cryptobiotes, able to survive temporary freezing or drying, than thermophiles having to evolve the genetic code and membranes beside oceanic vents in the enormous volumes of the deep ocean, as seems currently popular in some circles.”

“During the splicing process, mature mRNA, a very large cargo, appears to form a complex with a variety of distinct non-importin beta-type proteins that together mark the mRNA for export and participate in its egress from the nucleus. ... Indeed, it has been very difficult to confirm a specific translocation mechanism for the nuclear pore, which contains multiples of 30-50 different proteins in the final 500-1000 protein nuclear pore complex.”

“The discovery that RNAs could catalyze biological reactions gave a clear indication that RNAs would not conform to the Central Dogma, which dictates that they exist solely to relay information between DNA genes and protein gene products. Over the ensuing decades, RNAs have turned up unexpectedly as key players in myriad cellular activities, both fundamental and exotic. ... A new class of tiny noncoding RNAs (microRNAs) recently was implicated in developmental and spatial regulation of gene expression (Ambros, Cell 107, 823-826, 2001). Really, it would be surprising if nature has stopped here in making use of this versatile macromolecule.”

6. Molecular Machines: Ishii and Yanagida review Biology at the Single Molecule Level (ed. Leuba and Zlatanova, 2001) and show that the discovery of molecular machines is forcing a paradigm shift:

“The history of science has shown that new concepts frequently emerge and interpretations of the data become modified as more sophisticated and accurate measuring systems are developed. New data allow us to emphasize different aspects of biological systems and to reveal aspects of those systems that had not previously been unveiled. ... As nanotechnologies have expanded, many researchers have realized that the laws that govern materials of nanometer size are very different to those applied to macroscopic machineries with which we are more familiar. Nature, however, has already developed and utilized nanotech. Life is full of nanomachines, and their functions are very different from artificial nanomachines. ... Researchers now know that protein molecules are more complex than the simple design the DNA information implies. Studying the mechanism underlying protein functions is intriguing, and prerequisite are the techniques that allow us to monitor the dynamic structure of protein molecules and directly detect the functions of proteins.”

7. Homology and Evo-Devo Richard R. Behringer in “Hand of man, wing of bat, fin of porpoise” reviews The Evolution of Developmental Pathways by Sunderland (2002). He thinks Evo-Devo is the wave of the future:

“Biologists have always been fascinated by the astonishing diversity of metazoan life that has evolved on Earth. It is now evident that extant species have evolved from common ancestors through genetic changes that are acted upon by natural selection. In The Origin of Species (1859), Charles Darwin discussed the “law of embryonic resemblance.” He and others before him had noted that plants and animals within the same great classes, though morphologically diverse in their adult forms, were remarkably similar in their embryonic forms. For example, the limbs of vertebrates, including “the hand of a man, wing of a bat, and fin of a porpoise,” are morphologically and functionally distinct, yet they all develop from morphologically identical limb buds in their embryos. Darwin suggested that the embryos of different species provided a glimpse of a common parent for the different classes of organisms, supporting his concept of descent with modification. Thus was born the field of evolutionary developmental biology.”

He goes on to discuss the various controversies, questions, problems and conundrums in the field of evo-devo, but concludes it has a bright future thanks to television:

“Finally, the current movement in the Evo/Devo field suggests a bright future. That future may be driven by those children who watched natural history programs on television and have been inspired to pursue studies and careers in biology. I predict that these young biologists will not be satisfied studying a handful of primary model organisms. I suspect that these enlightened individuals will have broader interests and will be naturally attracted to the Evo/Devo field to reveal the “hidden bond” described by Darwin that exists between common ancestors and current species.”

8. From Cytoplasm to Cytoskeletons Don Ingber in “Putting the Cell Biology Establishment on the Stand” reviews Cells, Gels and the Engines of Life by Pollack (2001). He slays the dragon of misconceptions that the cell is simply a bag of fluid:

“While our knowledge of the molecular widgets that comprise living cells has exploded beyond our wildest dream, our understanding of cell architecture and the relation between structure and function still remain rudimentary. For example, one mainstream cell biology textbook defines the cell as “a small membrane-bounded compartment filled with a concentrated aqueous solution of chemicals,” like a balloon filled with molasses. In fact, many biologists who work with molecules in isolation still share this view, as do virtually all lay people, including the congressmen and women who decide which science projects the government will invest in.
Pollack views this image as a dragon that must be slain and I cannot agree more.”

“The living cell is a chemo-mechanical machine and it uses all forces and devices at its disposal-physical as well as chemical and electrical-to carry out its miraculous tasks. The reality is that the cytoplasm is a molecular lattice, known as the cytoskeleton, that is permeated and insufflated by an aqueous solution. The different molecular filaments that comprise the cytoskeleton-microfilaments, microtubules, and intermediate filaments-position the cytoplasmic organelles. But this is not a passive support system. The same scaffolds orient many of the enzymes and substrates that mediate critical cell functions, including signal transduction, glycolysis, protein synthesis, transport, and secretion; analogous insoluble scaffolds mediate RNA processing and DNA replication within the nucleus. This use of “solid-state” biochemistry greatly increases the efficiency of chemical reactions because they are no longer diffusion limited, and it provides a means to compartmentalize different cellular activities. The cytoskeletal system also can dynamically grow and shrink within different microcompartments as a result of the action of specific molecular regulators. ... Indeed, it is through these varied functions of the cytoskeleton that living cells can exhibit behaviors that are far beyond anything observed in man-made materials. The abilities of a cell to move its entire mass upstream against the flow of blood or contract against hundred pound weights are two simple examples.”

Tweaking the Bacterial Flagellum Motor 06/24/2002
A team of Japanese scientists publishing in the July 7 Journal of Molecular Biology has been studying the electrical interactions of the bacterial flagellum, a molecular motor highlighted in the film Unlocking the Mystery of Life. The researchers toyed with changes at the amino acid level in some of the key proteins in the rotor and stator to see what they would do. They neutralized or reversed the charges of elements and thought they would get the motor to halt, but in some cases, it reversed direction or continued to work, but reduced the tumbling behavior and swarming of the bacteria.

Different species of bacteria have different types of flagellar motors. Some run off protons (H+), and some run of sodium ions (Na+). The sodium motors spin up to five times faster than their proton counterparts. Earlier work had shown that mutations to a certain protein MotA in the proton motors could cause failure. These researchers mutated the homologous protein PomA in the sodium motor and still got it to work, so apparently there are other unknown factors involved in torque generation in these varieties.

How Does the Cell Route Messages? Through Its Switchboard 06/26/2002
Another “level of complexity” has been found in the cell, according to story in SciNews. Researchers at Johns Hopkins School of Medicine have found that signal transduction, the way that cells transmit signals from the external environment to the nucleus, is not just an automatic cascade of chemical reactions, but is regulated by a “switchboard” so that the nucleus is not swamped: “It’s a wonder cells make it through the day with the barrage of cues and messages they receive and transmit to direct the most basic and necessary functions of life.” The switching system involves first detecting messages coming through channels in the cell membrane onto receptors, then tagging them with one of two delivery signals, calcium or cyclic adenosine monophosphate (cAMP). A whole class of proteins called PDZ proteins are now seen to be involved just in deciding which signalling molecule will be used. The delivery tag determines how the nucleus will respond to the message. The study by Donowitz et al. into the tagging of messages for delivery into the nucleus was published in the June 20 issue of Nature. A related story about how the nucleus signals which genes to express is found on UniSci.

The New Science of Protein Sociology 06/27/2002
A news feature in Nature June 27 explores the new science of protein complexes:

“ ...the classic view of many cellular processes involves proteins interacting with one another in linear pathways, coming together as they shift around in the cell's cytoplasm. In recent years, however, biologists have realized that many important cellular functions are actually carried out by protein complexes that act as molecular ‘machines’”

The article explains that some complexes, like the ribosome, stay together for long periods, whereas others join loose fellowships for temporary tasks. Some proteins are versatile and belong to several clubs. In some cases, it is the complexes that are conserved between very different animals, but the individual proteins differ. New techniques of electron microscopy are allowing scientists to visualize these protein complexes in this cutting-edge field of structural biology.

Last edited by bob b; October 16th, 2006 at 04:32 PM.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Origami With RNA Requires Protein Chaperones 07/08/2002
RNA, like DNA, can easily form helical structures, and can also easily collapse into a muddled knot that is hard to untangle. For it to fold into useful structures, a group of proteins called chaperones are needed. The chaperones prevent the molecules from falling into “kinetic traps” that would be hard to unfold, and make sure they fold into the “native state”, the conformation that can perform the needed function in the cell. That’s the gist of a minireview in the June 28 issue of Cell. The article discusses several new findings, “a vindication of more than two decades of work on putative RNA chaperones and will almost certainly open productive new avenues for studying the management of RNA structure formation and processing in vivo.”

How Your Electric Motors Work 07/16/2002
Did you know your body, and the bodies of everything from bacteria to giant Sequoia trees, run on electric motors? No kidding. We’ve reported on the amazing little protein motor ATP synthase several times before. It runs at 6000 rpm and generates ATP, which your body needs for every chemical reaction, every muscle movement, and every blink of an eye. Now, in the July issue of the journal Structure, an international team of biochemists, including one of the winners of the Nobel Prize (Dr. John E. Walker), has examined the action of this amazing molecular machine in more detail than ever before. They have analyzed just one third of the rotational cycle of the top part of the motor, called F1-ATPase. The bottom part of this two-part motor, the F0 unit, is composed of a dozen parts that turn like a merry-go-round in response to proton fuel. Attached to the center is the gamma subunit that looks like a camshaft. It has a stalk and a protruding section that rotates with the F0 ring. In contact with the cam is the non-rotating F1 machine, composed of six lobes, the alpha and beta subunits, alternately arranged like slices of an orange around the central stalk. As the cam turns, it forces changes in shape of the alpha and beta lobes, mostly the beta lobes. Arranged in pairs, the six lobes provide a three-stage manufacturing plant for ATP; while one is loading the two ingredients, another is squeezing them together, and a third is simultaneously ejecting the finished product.

In this paper, the scientists carefully analyzed what happens to the alpha and beta subunits during one-third of the rotation. They found that the positive charges on the gamma protrusion (the cam) create an “ionic track”. Corresponding negatively-charged amino acids on the lobes, like motor brushes, respond to the ionic track by causing changes of shape in the lobes, making them move in, out, up or down appropriate to the stage of manufacture of ATP. Though the gamma shaft appears to turn smoothly, the lobes seem to snap open and shut very quickly, within nanoseconds. These “conformational changes” (i.e., moving parts) are involved in the efficient manufacture and release of ATP molecules; exactly how they do it is an area still under study. They do know, though, that the precise placement of certain electrically-charged amino acids in the various protein subunits stimulates the motions along the ionic track, so the cam involves both electrical and spatial (steric) interactions, something like a rotor in a car’s engine. The entire assembly operates at submillisecond rates, and is reversible – it can burn ATP to generate protons. The diagrams show that the motor parts look like coils, chains and complex tangles of molecules, not like the hard metal cylinders and pistons with which we are familiar, but they perform analogous functions at this submicroscopic scale. Even though the coiled amino acid chains twist and turn and stretch, the machine is stable, fast and highly efficient, The authors refer to it as a “finely tuned machine.”

Gene Expression More Complicated Than Thought 07/22/2002
Scientists used to think one gene produced one protein, and that a gene was an uninterrupted sequence of DNA code. No longer. Genes actually have coded regions, called exons, interspersed by non-coding regions called introns. There may be many introns per gene, and somehow the cell knows how to cut them out before making messenger RNA, which then delivers the code to the ribosome, where proteins are made. Are the introns just junk, then, destined for the cutting-room floor? Apparently not. The introns are involved in helping determine which exons get joined together, and by “alternative splicing,” the cell can get more mileage out of the gene. Some genes can code for several forms of a protein, depending on the order in which the exons are spliced together. Scientists at the University of California, Santa Cruz have developed new techniques to try to understand how cells make sense of all the pieces. Manuel Ares explains:

“The coding sequences of our genes are all broken up and spread out, and there is a whole cellular machinery involved in patching it together so that the code makes sense. This splicing process gives the cell the ability to try new combinatorial arrangements of information. You have all this information in the genome, but then the cell can interpret it in different ways.”

The press release says that genes are turning out to be much more complicated than originally thought. “Differences in the editing of genetic information may, in fact, be a significant source of genetic variability. Researchers ... have now taken a big step toward understanding how this editing process (known as splicing) is regulated.”

When Your Emergency Response Team Fails, Cancer Can Result 07/26/2002
Each cell in your body has a team of enzymes called DNA Damage Response. Like a skilled repair team, they know exactly how to fix all kinds of DNA emergencies: double-stranded breaks, broken tips, unraveled ends, and dozens of other potential problems. Many cancer cells exhibit unrepaired DNA and instability in the chromosomes. In a special section on genome stability in the July 26 issue of Science, Paula Kiberstis and Jean Marx explain that “For a cell, maintaining the integrity of its genome is of paramount importance. If it fails in this task and manages to divide anyway, both of its daughter cells may inherit an abnormal chromosome complement, with potentially dire consequences.” A current debate among biochemists revolves around whether the damage causes cancer, or the cancer causes the damage. They introduce three papers that deal with evidence that failures in DNA damage repair are implicated in many types of cancer, and conclude, “Whatever the outcome of these debates, the quest for answers has certainly produced many fascinating insights into the molecular weaponry that enables a cell to defend the integrity of its genome.”

Protein Evolution Recipe: Add a Pinch of Mutation and Stir 07/31/2002
In protein evolution, a lot of recombination mixed in with a little mutation provides the best results, say two scientists publishing in Proceedings of the National Academy of Sciences. Proteins, made of long chains of amino acids, have an uncanny ability to fold into just the right stable structure out of an enormous field of possible folds. How do they do it? How do proteins change through time and keep stable thermodynamically? For their mathematical model, Xia and Levitt simplified a three-dimensional problem down to two dimensions, and ignored population size and evolutionary time. They also used just short sequences – just 25 elements instead of the hundreds in most proteins. By adjusting the ratio of mutation to recombination, they were able to get sequences to converge on the “prototype sequence” (i.e., the largest set of sequences that folded into the same basic structure). This, they feel, may provide a solution to the “Levinthal Paradox” – “given the exponential size of the sequence space, how does evolution find the optimal sequence in a reasonable amount of time when the fitness landscape is flat?” They compare the ratio of recombination and mutation to temperature, and conclude: “Nature is able to adjust the ‘temperature’ of evolution by tuning the relative rates of recombination and mutation.”

Can We Live Without SMCs? No! 08/07/2002
That’s what Current Biology says in its Aug 6 issue in a feature entitled “Quick Guide to SMC Proteins.” OK, I give up. What are SMCs, and why do I need them?

“What are SMCs? The Structural Maintenance of Chromosomes (SMC) proteins are a family of chromosomal ATPases highly conserved among the three phyla of life. ...”

“What do SMCs look like? The SMC proteins are large polypeptides, each spanning 1000-1500 amino acids. They form dimers in which two anti-parallel coiled-coil arms are connected by a flexible hinge. ... The distal end of each arm constitutes an ATP-binding domain.”

If that didn’t help, what they are saying is that this family of proteins look like tweezers that can grab DNA and keep it under control during critical processes in the cell. The article then describes how these molecular machines work and what they do. They are important in holding sister chromatids together and separating them during cell division. Some are also “implicated in DNA repair and checkpoint responses.” They are also essential for the proper separation of chromosomes during gamete formation during meiotic cell division. So how do these miniature grappling hooks do all this?

“How do SMCs work? That is the million-dollar question in the field. Of particular interest is to understand how the two-armed structure - which is approximately 100 nm long when it’s open! - captures DNA, and how these interactions are modulated by ATP binding and hydrolysis. Condensin is able to introduce positive supercoils into DNA by using the energy of ATP hydrolysis. Further studies are required to understand the functional diversity of the SMCs.”

“Can we live without SMCs? No! Loss of any single SMC protein in budding yeast is lethal. Given their fundamental role in maintaining genomic stability, it is of future interest to determine whether loss or mutation of SMCs is associated with tumour formation or developmental disorders in mammals.”

The short article by Gillespie and Hirano (Cold Spring Harbor Laboratories, NY) contains a diagram of what two sample SMC proteins look like. The SMC “superfamily” work in complexes with other molecules to accomplish these vital tasks.

Siberian Bacteria Perform Repair in Deep-Freeze 08/20/2002Astrobiology Magazine claims that bacteria have been found that apparently are able to perform damage repair, even though they have been in a state of suspended animation in deep freeze for up to tens of thousands of years. Indirect methods suggest that these bacteria maintain a high ratio of left- to right-handed amino acids; if dead, the ratio would approach 50/50 over time. Cells need pure 100% left-handed amino acids to function. Because radiation even within the ice would cause damage to DNA and other essential molecules over time, Gene McDonald at JPL and colleagues feel that a certain amount of repair must be in operation, even in the deep freeze of Siberian permafrost. This gives them hope that any Martian organisms might have survived billions of years of freezing, even if changes in the environment sent them into hibernation.

How Do Leaves Prevent Meltdown During Photosynthesis? 08/22/2002
We all know plants harvest sunlight for energy, but what do they do when the energy is coming in too fast? Imagine coal lumps on a conveyor belt coming into a furnace. Unless there is a way to regulate the furnace, too much coal will make it overheat. Plants, it turns out, have multiple feedback loops and regulatory processes to prevent damage when the photons are coming in too fast. Scientists at Washington State studied one of these regulatory processes called nonphotochemical quenching (NPQ) and published their results in the Proceedings of the National Academy of Sciences. Although not completely understood, NPQ involves making the ATP synthase motors in the chloroplast less reactive to the flow of protons coming in. This requires high sensitivity to the acidity (pH) of the lumen, the light-harvesting portion of the chloroplast, and is regulated early in the process:

“Furthermore, the pH of the lumen appears to be tightly regulated to a narrow range, where the stabilities of luminal components and the effective rate constants for electron transfer are near optimal. Taken together, these observations indicate that a primary regulatory step governing light energy conversion must occur at light capture, and thus likely involves NPQ, rather than at downstream electron or proton transfer reactions.”

NPQ is also very sensitive to the amount of carbon dioxide in the atmosphere. Taken together, these regulatory controls keep the ATP synthase motors from being overloaded with protons.

We’ve reported on ATP synthase several times, the tiny rotary motors that manufacture energy pellets (ATP) for the cell. They are powered by proton motive force generated by photosynthesis in plants and by metabolism of food in animals, ultimately from sunlight in both cases. In another paper in the current issue of Cell entitled “Photosynthesis of ATP–Electrons, Proton Pumps, Rotors, and Poise,” John F. Allen mentions these motors in a review of how electrons are cycled around during photosynthesis. In addition to praising photosynthesis as the food source for all life, he comments, “Photosynthesis is also responsible for the global redox imbalance now seen as abundant, free oxygen–our planet’s signature of life, unique in the solar system.” His illustrations of ATP synthase and the other components involved in photosynthesis, though just models, look for all the world like power plants and storage batteries connected by wiring.

Mitochondria Challenge Evolutionary Speculations 08/26/2002
The Scotsman reports on a paper in Nature Aug 23 (see also News and Views analysis) that challenges the long-held theory that mitochondria were captured by early eukaryotes and became symbiotic with them. Evidence of mitochondrial parts have been found in microsporidia, a primitive parasite thought to lack mitochondria. They appear to be shrunken remnants of the organelles, degenerated perhaps due to the parasite’s energy needs. Dr. John Lucocq of Dundee University where the discovery was made remarked, “This discovery changes the way we think about how cells evolved. If these parasites are a sort of living fossil, then this is a bit like a ‘missing link’ human ancestor turning out to be a present day human.”

Another story on the mitochondria in New Scientist reports that contrary to conventional wisdom, mitochondrial DNA can be inherited from both parents. “Evolutionary biologists often date the divergence of species by the differences in genetic sequences in mitochondrial DNA. Even if paternal DNA is inherited very rarely, it could invalidate many of their findings,” says the article.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Elegant, Intricate, Remarkable Describe Cell Channels 09/05/2002
Gary Yellen of Harvard, in a review article in the Sept 5 Nature waxes prosaic while describing the voltage-regulated channels in cell membranes: with words like “remarkable” and “elegant” he describes the ongoing research into the gatekeepers of the cell:

“The remarkable optimizations of these channels for permitting rapid and selective ion flow across the hostile barrier of the cell membrane are now mostly apparent, as is the basic repertoire of conformational changes used to gate this flow. We now see the outlines of two general approaches used by intracellular sensor domains to manipulate the channel gates, and some tantalizing details of the transmembrane voltage sensor itself. “

The potassium channel is capable of passing millions of potassium ions per second through its “selectivity filter” while keeping out sodium ions, smaller and with the same charge. How it does this is on the leading edge of research. Apparently several mechanisms are involved. The channel is able to mimic the arrangement of water molecules that naturally assemble around the ions, and guide them through the channel single file. Also, parts of the channel rapidly flex open and closed in response to the ions or to voltage sensors. A delicate balance of electric charge is required to attract the ions yet prevent them from sticking in the channel. Several ions at a time can be passing through, each validated by the selectivity filter. All this is regulated by voltage sensors, still poorly understood. Cell signalling and nerve impulse transmission rely on the quick and accurate electrical transduction performed by these tiny gatekeepers. An additional wonder is how the channels cooperate with each other, so that an electrical impulse lasting just a few milliseconds can be transmitted at a speed of several meters per second from your toe to your brain. “Electricity plays an unavoidable role in biology,” Yellen opens his article, as he describes how animal cells “have made the management and production of electrical signals into a high art.”

Peering Into a Tiny Machine on Which the World Depends 09/06/2002
Sometimes it’s the little things that count. World food supply, ecology, biodiversity are big things, but they depend heavily on a tiny molecular machine called nitrogenase. This machine is worth its weight in gold and is the envy of chemical and structural engineers, but it makes its home in the lowliest of organisms, little bacteria that live around the roots of plants. Its job? To break apart the triple bonds of atmospheric nitrogen molecules and make them available as ammonia to plants, which use this valuable fertilizer to produce proteins for the entire food chain. Molecular nitrogen (N2), though plentiful in the atmosphere (78%) is useless until “fixed” by breaking it apart and combining it with hydrogen as ammonia (NH3). Given plenty of water, nitrogen is the usually the limiting factor in agricultural food production. About half the world’s ammonia is produced by these tiny machines. A little is fixed naturally by lightning, indicating the high energy required. The rest, manufactured by man in the expensive Haber-Bosch process, consumes an estimated 1% of the world’s annual energy output. Those triple bonds are tough nuts to crack! How do the nitrogen-fixing bacteria do it so efficiently, at ambient temperature and pressure? Whoever figures this out and imitates the process will enrich the world’s food supply and save trillions of dollars.

Scientists have been sharpening the focus more and more on this tiny protein machine, nitrogenase. They knew that precisely placed metal ions (iron, molybdenum) form a critical structure in the heart of the enzyme. They knew other proteins spend ATP to donate electrons to the nitrogen. Now, writing in the Sept. 6 issue of Science, a team of American scientists has sharpened the focus down to 1.16 angstrom resolution. One surprise was that they detected another atom, possibly atomic nitrogen, deep in the heart of the active site. How it gets there, and what role it plays, is still a mystery, but this is another important piece of the puzzle. In the same issue of Science, Barry Smith summarizes the work and concludes, “Once again, nitrogenase has surprised us.”

More Complex Than Anyone Ever Dreamed: Cell Quality Control 09/09/2002
According to NewsWise, biochemists like Lynne Maquat at the European Molecular Biology Organization are looking into tinkering with the cell’s quality control system to see if certain error-correcting mechanisms can be switched off. This might provide a means of testing new drugs or treating genetic diseases. In discussing the work, the article uses superlatives to describe how the cell usually corrects mistakes :

“...mistakes, which are eliminated by dogmatic quality control. ... mRNA molecules are like messengers in a factory, taking a blueprint and then heading to the floor and gathering a team to get the job done. Sometimes, though, the mRNA doesn’t quite get the message right. One common error happens when an mRNA molecule harbors a “stop” or “nonsense” signal before a protein has been completely made. Enter the body’s quality-control system. ... nonsense-mediated decay targets what scientists call a “pioneer round of translation,” during which the body actually produces a kind of rough draft of a protein before giving the go-ahead to the mRNA molecule to begin mass production. ... mRNA puts together an extensive tool kit of molecular machinery to evaluate whether it should pass muster as a legitimate template for proteins. ...
The identification of such “tool kits,” groups of molecules working together to achieve a task, keeps hundreds of lab groups like Maquat’s around the world constantly busy. Far from the simple and bland “DNA to RNA to protein” sequence of events that many people learn in high school, nearly every cell in the body embodies an incredibly complex construction site where tens of thousands of proteins work in tandem, snipping and cleaving molecules, removing “introns” and splicing together “exons” in various combinations, recruiting molecules to the site, and ferrying molecules over to ribosomes for assembly into proteins. ... “There’s an incredible amount of activity in a small space,” says Maquat, who is secretary/treasurer of the RNA Society and who organized a meeting this summer on the topic of mRNA decay for the Federation of American Societies for Experimental Biology. “A single gene can result in many different proteins depending on how its encoded precursor mRNA is processed; we now know that more than half of human genes can make more than one protein. But with this wonderful flexibility often comes mistakes. The situation is turning out to be more complex than anyone ever dreamed. The degree of RNA processing that the cell undertakes is truly amazing.” The idea of trying to bypass the body’s mRNA surveillance system is formidable. Maquat notes that the system is necessary for survival, and that without it, bad mRNA would create even more instances of disease.”

Though a formidable prospect, she and her team hope that by allowing some mRNAs to sneak past the quality control guards, some genetic diseases might be treatable, and the process might open up “new vistas for pharmaceutical companies.”

The Spliceosome: The Most Complex Cellular Machine Yet 09/12/2002
A molecular machine with 4 RNAs and 145 proteins: that’s the spliceosome, writes a team of Harvard biochemists in September 12 Nature. Its job? “The precise excision of introns from pre-messenger RNA is performed by the spliceosome, a macromolecular machine containing five small nuclear RNAs and numerous proteins.” Why higher organisms have so many introns (non-coding regions of DNA) and smaller exons (coding regions), and how the exons are joined, is on the cutting edge of DNA research. Formerly considered “junk DNA,” the introns seem to play an essential role in gene expression. They also may provide flexibility for coding regions to join in multiple ways, extending the information content of the DNA. In any event, the splicing of exons together correctly has little tolerance for error, and the spliceosome helps ensure that an accurate messenger RNA gets built before being sent to the ribosome, where the protein product will be assembled. “...we identify 145 distinct spliceosomal proteins,” they announce, “making the spliceosome the most complex cellular machine so far characterized.” Furthermore, the authors find that this machinery is highly conserved (unevolved) between yeast and metazoans [multicellular organisms], including humans:

“The potentially greater complexity of the human spliceosome is not unexpected in light of the vastly greater complexity of splicing in metazoans compared to yeast. Indeed, most metazoan pre-mRNAs contain multiple introns, the introns are typically thousands of nucleotides, and the splicing signals are weakly conserved. Superimposed on this complexity is the high frequency of alternative splicing, which is in turn further complicated owing to regulation. Thus, many of the metazoan-specific proteins may play roles in the accurate recognition and joining of exons.

Another paper by German biochemists in the same issue of Nature announces a newly-found role of a chaperone protein named L23. This protein sits at the exit tunnel of the ribosome and forms a docking station for other chaperone proteins, which then grab the emerging polypeptide and fold it properly into its unique shape to become a functioning protein.”

In the following week’s issue of Nature (Sept 19), Canadian scientists found evidence of introns and splicing machinery in a primitive eukaryote, adding more evidence that spliceosomal introns “are likely to have arisen very early in eukaryotic evolution.”

Here we see another complex molecular machine, composed of nearly 150 coordinated parts, that operates with skill and precision. “Spliceosomes undergo multiple assembly stages and conformational changes during the splicing reaction,” say the authors, indicating that these machines have many moving parts. They conclude with an acknowledgement that the cell is a veritable factory of complex machinery:

“The observation that the spliceosome is associated with numerous proteins that function in coupling splicing to other steps in gene expression provides compelling evidence for the emerging concept of an extensively coupled network of gene expression machines.”

Genetic Code is Even Parity 09/12/2002
Did you ever learn about even and odd parity in computer class? If so, you know that parity bits are often added to computer codes to reduce errors. If the receiving end reads a byte that is odd when it is supposed to be even, it knows there has been an error. Dónall Mac Dónaill, a chemist at Trinity College Dublin, thinks that DNA uses this technique in the genetic code. He asked why, of all the possible nucleotides, DNA only uses A, C, T, and G. Examining the molecules, he noticed that these four seem to have “even parity.” This makes them very unlikely to pair with the wrong base. An Oxford computational chemist thinks this is a potentially fruitful concept: “It is a novel idea which should provoke others to explore aspects of informatics in the genetic code,” says Graham Richards. The story is summarized on Science Now, and also on Mac Dónaill’s website, and Nature Science Update explained the idea on their site on Sept. 18, emphasizing that “The consequences of wrongly read or copied information can be disastrous. Malfunctioning genes can cause diseases and defects.”

Primordial Soup Cannot Tolerate Salt 09/17/2002
In what appears to be a devastating blow to beliefs that life first appeared in the oceans, scientists at UC Santa Cruz, publishing in the journal Astrobiology Vol 2. No. 2 (2002) have experimented with what salt does to RNA and membranes. They found that sea salt destroys fatty-acid membranes and prevents RNA from forming chains (polymerizing), even at concentrations seven times weaker than in today’s oceans. The ingredients of sea salt are very effective at dismembering membranes and preventing RNA units (monomers) from forming polymers any longer than two links (dimers). Noting the “exceptional properties of contemporary cellular membrane structures,” they emphasize that without some kind of osmotic control, primitive vesicles would have collapsed in the presence of divalent cations such as are present in sea salt. Even if early oceans were far less salty, the prebiotic compounds would have needed to be concentrated. But as they logically point out, “Concentrating mechanisms often have a drawback in that they are not selective. That is, not only monomers but also any ionic solute present will be concentrated,” including the damaging salts.

Considering their study a “crucial piece of information” for origin of life studies, they conclude that the origin of life in the oceans would not be possible, and that a very protected environment of fresh water on the continents would have been necessary for emergent life to evolve far enough to protect itself from the damaging effects of sea salt: “In this very protected environment, simple protocellular entities could thrive until the evolutionary appearance of a primitive metabolic machinery and active salt transport systems in membranes allowed them to overcome the disruptive impact of more saline environments.” The paper is entitled, “Influence of Ionic Inorganic Solutes on Self-Assembly and Polymerization Processes Related to Early Forms of Life: Implications for a Prebiotic Aqueous Medium,” by Monnard, Apel, Kanavarioti and Deamer.

Motors in Your Ear Amplify Sound 10,000-Fold 09/19/2002
What limits the hearing range in the ear? Apparently not the eardrum or bones of the middle ear, but the cochlea in the inner ear. We reported in February about prestin, the speedy molecular motor that is involved in controlling the volume of sound on the hair cells of the cochlea. Now, scientists writing in the Sept. 19 issue of Nature have confirmed that prestin is the primary agent in the control of sound amplification, or at least that no other mechanism is necessary to explain the observations. In their research paper entitled, “Prestin is required for electromotility of the outer hair cell and for the cochlear amplifier,” they explain that this little molecular motor, that affects the stiffness of outer hair cells responding to sound waves, provides a 40-60 decibel increase in sensitivity of the ear: a factor of one to ten thousand. By knocking out the prestin motor in mice, the scientists observed a 10,000-fold reduction in hearing sensitivity.

Scientists Fold a Small Protein 09/25/2002
According to Nature Science Update, scientists were able to calculate the fold of a small protein of 20 peptides just from knowing its amino acid sequence. The synthetic protein folds into a tight structure like real proteins; “most short chains remain loose and floppy,” the report states. The team used computer simulation to predict the fold that actually occurred, measured by nuclear magnetic resonance spectroscopy. The difficulty in predicting the fold grows exponentially, however, with length of the sequence, and most proteins are hundreds of amino acids long. The precise fold of a protein is essential to its function. Understanding and predicting protein folding from just the amino acid sequence is one of the most formidable challenges facing biochemists. On a related subject, a paper in the Sep. 25 preprints of the Proceedings of the National Academy of Sciences discusses some of the many diseases that occur when proteins do not fold correctly.

Shipping Labels Used on Cell’s Cargo 09/26/2002
Bound for New York? Read the label. Destined for the trash can? Read the label. Just as Federal Express or any other shipping company depends on labels to keep myriads of packages on target to equal myriads of destinations, the cell tags its cargo with molecular labels to keep everything on track. Nature (Sept. 26) has two articles on this topic that explain how the cell does it. In The Making of a Vesicle, Anne Schmidt describes work by Ford et al on a protein tag called epsin that stimulates a membrane to curve around, or “package” a piece of cargo for shipment, such as nutrient uptake or removal of parts from the cell surface.

In another News and Views article, Keith Wilkinson in “Unchaining the condemned” describes how the cell labels obsolete cargo for the recycle bin. Apparently, the protein tag called ubiquitin (which is truly ubiquitous in all eukaryotic organisms) tells the proteasome (the recycle bin) that this cargo is ready for dismantling and salvage. Wilkinson explains:

“To carry out their functions properly, the proteins in our cells must be in the right place at the right time, and at the right concentration. So it’s vital that cells achieve the correct balance between protein synthesis and destruction. Although we understand much about how proteins are made, it is only in the past ten years that we have come to appreciate the complexity of their degradation. Like everything else, proteins outlive their usefulness and, whether damaged or just no longer needed, they are often condemned to destruction by the covalent attachment of another protein, called ubiquitin. When this process fails, it has profound consequences for events such as cell division, gene expression and the development of cancer.”

Wilkinson presents the work of Yao and Cohen that indicates that one ubiquitin tag means sort, and several means recycle. The rest of the cell must understand the tag to know what to do, and the proteasome (shaped like a narrow tunnel) has to remove the labels before doing its grisly work.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Do Enzymes Evolve From Nonenzymes? 10/02/2002
A paper in the Oct. 2 issue of Structure compared enzymes with nonenzyme homologs to see if either had evolved into the other. In “Sequence and Structural Differences between Enzyme and Nonenzyme Homologs,” three UK women biochemists have no doubts that evolution has shaped enzymes into their repertoire of functions: “Ancestral genes have been duplicated, mutated, and combined through evolution to generate the multitude of functions necessary for life.” Yet deep in the paper, it is clear that most of their findings show that most homologs appear to have lost enzymatic function: “The examples presented suggest that the evolution of a nonenzyme from a catalytic precursor is more common than the reverse scenario, that is, the design of a catalytic function on an ancient nonenzyme domain.” They found 12 examples of enzymes losing catalytic function, and five of nonenzymes gaining it; but “In all five ‘nonenzyme to enzyme’ examples ... nature appears to have exploited the specific binding properties of the catalytically inactive precursor.”

Your Immune System: How the Assassins Recognize the Terrorists 10/03/2002
Killer T cells, like roving assassins in a search and destroy mission, look for viral terrorists and obliterate them in their hideouts. But first they have to recognize who is friend or foe, and in auto-immune diseases or tissue rejection, sometimes mistakes are made. How the cell flags its contents, and how the T cell detects it and responds, is a complex and mysterious process. Scientists are nearing completion of understanding the general picture from start to finish. One question that remained was how a system that is highly conserved from mice to men could produce a unique “scent” at the cell surface, so individual that your immune system can sense the difference between “you” and “foreign.” An important piece of the puzzle has recently been identified and reported in the Oct 3 Nature by U.C. Berkeley biochemists. But to understand it, we have to back up and create some word pictures, or else get bogged down in abstruse jargon. Pardon us in advance for the silly analogies and mixed metaphors; the reality is really quite amazing.

Killer T cells recognize body cells infected with a virus because each cell has a sophisticated system of wearing its innards on the outside. An individual cell can have about 10,000 flags on its surface, composed of pieces of every protein found in the interior. These flags, like sausages always nine amino-acid links long, are mounted on flagpoles, or rather meatpoles, called MHCs. How do they get there? Well, as proteins inside outlive their usefulness and are tagged for recycling, a barrel-shaped meat cleaver called a proteasome chops them into sausages up to 15 units long. Sent back into the cell, most are quickly seized upon by roving dogs (aminopeptidases), but some manage to make it into the subway (endoplasmic reticulum) through special mechanical gates made just for them (TAP, for “transporters associated with antigen processing”). There, another cleaving machine starts dismantling them one link at a time. Crowded nearby are MHCs looking for the unique nine-unit pieces that fit them just right. When no match is found, the chopper keeps cutting the links all the way down for recycling. But if an MHC finds a nine-unit sausage that matches perfectly, it mounts it and ferries it to another special porthole on the cell surface, where it plants it to wave in the breeze. A killer T cell, roving about with a nose that makes a bloodhound look like a man with a bad cold, sniffs all these pieces of meat and is able to detect foreign meat (viral protein scraps) that are not “USDA approved” so to speak. If it finds one, the penalty is severe: the whole cell is targeted for incineration. But it’s a small price to pay for health of the body. This is a nonstop state of war and the stakes are high. Any cell that harbors terrorists must be destroyed. Besides, there are trillions more cells that can take their place.

What these scientists found was the chopper (aminopeptidase) in the subway that trims the sausages down. They named it ERAAP, and found that it does not need to be concerned with fitting each nine-link sausage to the appropriate meatpole (MHC); it just chops away, one link at a time, and if an appropriate meatpole is nearby to grab it, fine. If not, it chops it all the way down and the individual links (amino acids) are made available for recycling into new proteins. In his News and Views perspective on this discovery, Hans-Georg Rammensee calls this “Survival of the Fitters” – “the way ERAAP works is a fine example of how nature uses the survival-of-the-fittest principle, even inside the cell, to solve a complex task in an economical way.”

Cell Beats Computer: 100 Trillion Times Faster at Folding a Simple Protein 10/15/2002
Researchers at Los Alamos National Lab modeled the folding of a “simple” protein of 18,000 atoms on their computers, reports EurekAlert. It took 6 months on 82 parallel processors, which amounts to 34 years of CPU time. The cell folds this particular protein in about 10 microseconds (millionths of a second), which is 100 trillion times as fast. That’s proportional to one second vs. 3.4 million years. The computer algorithm the scientists designed “relies on exhaustive sampling of protein configurations and utilizes massively parallel computing combined with molecular dynamics and a random-sampling Monte Carlo simulation of the thermodynamics.” It is expected that the processing time would grow exponentially with the increasing length of the protein chain, but cells routinely fold their proteins within milliseconds to microseconds. University of Florida reports a record holder: a short 20 amino acid protein that folds within 4 microseconds. Biophysicist Stephen Hagen asks, “What is it that’s special about these molecules that enables them to solve a very difficult computational problem spontaneously in such a short amount of time?”

Update 10/21/2002: Nature Science Update reports that a scientific team predicted a protein fold successfully by using spare time on 200,000 home PCs in a distributed project called Folding@home. This amounted to about to 2,000 years of computer time. The article states, “Trying to anticipate how the many atoms within a protein interact as it crumples up is a mind-bending problem – involving near a billion steps. Like entering a maze, the molecular backbone can start looping up in a [sic] numerous different ways, yet most paths lead to dead ends.” Somehow the real protein avoids the pitfalls and finds shortcuts through the maze, achieving its correct shape in five milliseconds.

Announcing: The Protein Big Bang Theory 10/16/2002
A paper in the Oct 16 online preprints of the Proceedings of the National Academy of Sciences has an intriguing title: “Expanding protein universe and its origin from the biological Big Bang.” Three biochemists from Harvard, University of North Carolina School of Medicine and Boston University attempted to demonstrate a “possible origin of all proteins from a single or a few precursor folds a scenario akin to that of the origin of the universe from the Big Bang.” A striking characteristic of biological proteins is that many have similar folds even with unlike sequences of amino acids; these are called “orphans” because they are nonhomologous: i.e., they appear to have no common ancestors. To explain this, previous investigators imagined that there might be some kind of designability principle that made evolving proteins converge on these special folds. This team set out to show that biological proteins could have diverged instead from simple random precursors; in other words, divergent evolution rather than convergent evolution produced the protein domain. To do this, they graphed all known protein folds on what they call a “protein domain universe graph” (PDUG), tweaked in such a way as to make it scale-free. (An example of a scale-free network is the world-wide web.) After differentiating it from random networks, they deduced that it could have grown by divergent evolution, as proteins evolved through recombination, duplication and mutation, such that folds were preserved even as the sequences were shuffled:

“It is quite suggestive that the origin of the observed scale-free character of the PDUG lies in the evolutionary dynamics of protein fold genesis as a result of divergent evolution from one or a few precursor domains. To this end, we develop a minimalistic model that aims to explain the scale-free PDUG. Specifically, we assume, as do several other models, that new proteins evolve as a result of an increase in the gene population primarily by means of duplication with subsequent divergence of sequences by mutations, as well as more dramatic changes such as deletions of certain parts sequences and even possible reshuffling of some structural elements (foldons).”

Their analysis yielded a striking number of orphans, as expected, giving them confidence in their analysis. They caution, however, that the picture is oversimplified:

“The divergent evolution model presented here is a schematic one, as it does not consider many structural and functional details, and its assumptions about the geometry of protein domain space in which structural diffusion of proteins occurs may be simplistic. However, its success in explaining qualitative and quantitative features of PDUG supports the view that all proteins might have evolved from a few precursors.”

They conclude by also cautioning that their graphical analysis was just an algorithm selected to “spy” on nature, not that nature used any algorithm to create the protein domain. They chose the algorithm and set the threshold values to attempt to discern natural processes from random ones.

Ancient Cell Wiser than Most Computer Users 10/23/2002
The agony of delete strikes many computer users who neglect to back up their data, but an ancient one-celled organism apparently has the wisdom to keep backup copies of its genome. That’s the implication of a story in the BBC News about Tetrahymena, a primitive protozoan that has a macronucleus with the working genome and a micronucleus with a master backup copy. Martin Gorovsky of the University of Rochester has studied this ancient lifeform’s strategy to protect its DNA:

“Gorovsky’s team believes that in evolutionarily ancient times, cells had to fight against a variety of assaults just as they must today: viruses attacked cells, injecting their DNA to disrupt normal cell functions; and transposons, bits of nomadic genetic material that insert themselves into the cell’s DNA causing havoc. To survive, cells evolved a correction system that recognized the invading DNA and either eliminated or silenced it.”

The team found that Tetrahymena inspects its DNA against the master copy before passing it on, to ensure the progeny get an uncorrupted copy. Gorovsky suspects a similar defense mechanism is at work in higher organisms.

Plants Borrowed Membrane Channels 10/25/2002
All living cells have specialized membrane channels that allow certain molecules in and keep others out; for water, they are called aquaporins (AQPs); for glycerol, they are called aquaglyceroporins (GLPs). There are also ion channels for chloride or potassium. The set of channel families are called membrane intrinsic proteins (MIPs). An international team of researchers has compared the channel proteins from plants, bacteria, and animals, and deduced that plants got their glycerol channels by horizontal gene transfer, with subsequent modification by functional recruitment:

“The molecular phylogeny of MIPs supports that glycerol transporting in plants was acquired by horizontal gene transfer and functional recruitment of bacterial AQPs. It is likely that these events were triggered by the absence of a GLP homolog in the common ancestor of plants. We find that plant NIPs and GLPs share convergent or parallel amino replacements needed to transport glycerol and therefore represent a remarkable example of adaptive evolution at the molecular level.”

Their paper is published in the Oct. 23 preprints of the Proceedings of the National Academy of Sciences.

Fix the Textbooks: Cyanobacteria Weren’t the First 10/25/2002
“Get ready to rewrite those biology textbooks - again,“ begins the article on EurekAlert based on a story from the Geological Society of America, entitled “Evolution upset: Oxygen-making microbes came last, not first.” A researcher named Carrine Blank from Washington University found that cyanobacteria are too highly evolved to have been the first critters. But “If Blank is correct, her revised evolutionary history of the bacteria raises a difficult question: If cyanobacteria came later, where did the Earth’s earliest oxidants come from which produced banded iron formations?”

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Two For the Price of One: Did Transfer RNA Arise From Complementary Genes? 11/01/2002
The latest (Oct 27) issue of Molecular Cell has a novel theory on how transfer RNA evolved. In a letter to the editor, Charles Carter and William Duax revive the 1995 Rodin-Ohno hypothesis that suggests complementary strands of DNA can code for different proteins. To understand this, we need to back up and learn a little about transfer RNA. DNA translation, you may recall, starts when enzymes unwind a strand of DNA to expose a gene, and a messenger RNA molecule forms by base-pairing with the exposed DNA nucleotides (the “letters” A, C, T, and G). The resulting messenger RNA molecule (mRNA), like a long computer tape bearing the code for a protein, exits the nucleus and approaches a ribosome. There, individual transfer RNA molecules (tRNA), each carrying a specific amino acid on one end and a three-letter RNA codon on the other, mate with specific parts of the mRNA by base-pairing, and the amino acids on the other end join together into a protein chain. This much is elementary biochemistry, illustrated beautifully with computer animation in the film Unlocking the Mystery of Life. The process is actually much more complicated, requiring a host of helper enzymes at every step.

One set of helpers that is extremely critical to the accuracy of the operation comprises the aminoacyl-tRNA synthetase family (aaRS). These are the enzymes that join the appropriate amino acids to the transfer RNA molecules. There are 20 of these aaRS enzymes, one for each of the 20 types of amino acids used in proteins. What is most interesting and amazing about them is explained by James F. Coppedge in his book Evolution: Possible or Impossible?:

“There seems to be no natural attraction between an amino acid and its own transfer-RNA, so something must bring them together. It is as if there were two languages, and neither party understands the other except when there is an interpreter to bridge the gap. This essential task is done by a special group of enzymes which match the different tRNA’s and amino acids. One part of each such enzyme fits just its own particular kind of amino acid and no other. Another part of the enzyme interacts with its own type of tRNA. In plain language, it can be pictured as follows: the enzyme grasps its amino acid and its tRNA and fastens them together. (p. 147)

In the Molecular Cell article, Carter and Duax recognize the challenge that this complex arrangement presents to evolutionary theory :

“The fidelity of protein synthesis resides almost entirely in the 20 aminoacyl-tRNA synthetases (aaRS), which acylate their cognate tRNAs with the appropriate amino acid. The origin of codon-dependent translation presents a challenging intellectual problem in biology, owing to the apparently irreducible complexity represented by their simultaneous appearance. Key to the conundrum is that contemporary aaRS divide into two classes each with ten enzymes (Eriani et al., 1990 ), whose respective architectures have quite unrelated homologies (Cusack et al., 1990 ). Moreover, catalytic domains in class I and II aaRS:tRNA complexes from corresponding subclasses have complementary shapes that recognize nonoverlapping surfaces on the tRNA acceptor stems (Ribas de Poublana and Schimmel, 2001 ). Pairwise binding between classes may therefore have protected tRNAs early in evolution, and the class division likely dates from the dawn of biology.”

Drawing from an analogy with a gene found in a freshwater mold that seems to code for two different proteins, depending on whether the primary strand of the gene or its complementary strand is translated, Carter and Duax propose that genetic complementarity is behind the origin of the two classes of aaRS enzymes: one class evolved off the primary “sense” strand of DNA, and another class evolved off the complementary “antisense” strand. From the original primordial split, the 20 aaRS enzymes arose: “Two synthetases, coding from that repertoire, might similarly have sufficed to produce recognizable protein folds. Subclass speciation via gene duplication then would have enriched the coding repertoire.”

Cell Memory “Borders on the Miraculous” 11/04/2002
Just when you thought the DNA code was mind-boggling enough, along comes the histone code. Another coding system somehow helps the cell remember itself: whether it is a blood cell, or a nerve cell, or a muscle cell. While all these cells in your body have the same genetic code, some kind of epigenetic (above-gene) code is telling it what genes need to be turned on. The Nov. 1 edition of the journal Cell has a review by Bryan M. Turner of the University of Birmingham (UK) called “Cellular memory and the histone code” that waxes enthusiastic about this cutting-edge mystery :

“It is an obvious but easily forgotten truth that cells must have a mechanism for remembering who they are. A cell’s identity is defined by its characteristic pattern of gene expression and silencing, so remembering who it is consists of maintaining that pattern of gene expression through the traumas of DNA replication, chromatin assembly, and the radical DNA repackaging that accompanies mitosis [cell division]. The mechanisms by which around 2 m [two meters, about 6 feet] of DNA is packaged into the cell nucleus while remaining functional border on the miraculous and are still poorly understood. However, we do know more about the first stage in this packaging process, the nucleosome core particle. This structure comprises an octamer of core histones (two each of H2A, H2B, H3, and H4), around which are wrapped 146 base pairs of DNA in 1 3/4 superhelical turns (Luger et al., 1997 ). The reduction in DNA length produced by this histone-induced supercoiling is modest, but is an essential first step in the formation of higher-order chromatin structures. In recent years it has become clear that the nucleosome has an additional role, perhaps equally important and conserved, namely regulation of gene expression. Particularly exciting is the growing probability that the nucleosome can transmit epigenetic information from one cell generation to the next and has the potential to act, in effect, as the cell’s memory bank.”

Turner describes how the histones have tails that are exposed on the exterior of the nucleosome. It is on these tails where a variety of enzymes can rearrange some of the amino acids, providing a “rich source of epigenetic information.” So how is the code maintained and translated?

“It has been suggested that specific tail modifications, or combinations thereof, constitute a code that defines actual or potential transcriptional states (Jenuwein and Allis, 2001; Richards and Elgin, 2002; Spotswood and Turner, 2002). The code is set by histone modifying enzymes of defined specificity and read by nonhistone proteins that bind in a modification-sensitive manner. In order to realize its full information carrying potential, the code must use combinations of modifications. This requires not only proteins that can read such combined modifications, but mechanisms by which they can be put in place and maintained. Recent papers have provided new insights into how specific combinations of tail modification might be generated and revealed mechanisms by which the modification of one residue can determine that of another.

Turner discusses in some detail the types of reactions already known and puzzles that remain to be solved. The histone code appears quite different from the DNA sequence of letters; it is more a sequence of events: “Viewed in this light, the histone code can be seen as part of a sequence of events, possibly involving structural and catalytic proteins and RNAs, whose end result is a functionally stable chromatin state.” At times in the article the complexity of all of this seems to get to him; “To add further complexity,” begins one sentence. Near the end, Turner remarks wryly, “It is in the nature of scientific progress that simple ideas, like people, grow more complex with age.”

Defective Proofreading Causes Cancer 11/12/2002
Scientists at University of Utah School of Medicine mutated genes in mice responsible for proofreading DNA, and saw 94% of them get cancer. Writing in the Nov 12 online preprints of the Proceedings of the National Academy of Sciences, they stated, “Mutations are a hallmark of cancer. Normal cells minimize spontaneous mutations through the combined actions of polymerase base selectivity, 3'-5' exonucleolytic proofreading, mismatch correction, and DNA damage repair.” They induced a point mutation in DNA polymerase delta, one of the molecular machines with a proofreading domain, and the high incidence of tumors resulted. Only 3-4% of the mice without the mutation developed cancers.

DNA Translator Does the Twist 11/16/2002
A molecular protein machine responsible for translating DNA in a “primitive” cell does some pretty amazing gymnastics, scientists have discovered. Writing an extended research paper in the Nov 15 issue of Science, two biochemists from the Howard Hughes Medical Institute (Yim and Steitz) found that the RNA Polymerase (RNAP) of T7 bacteriophage is quite the contortionist. Lacking the larger genome of eukaryotes, its DNA translation equipment has to get by with less, so it performs three large conformational changes on one end, and additional shifts on the other: “The transition from an initiation to an elongation complex is accompanied by a major refolding of the amino-terminal 300 residues. This results in loss of the promoter binding site, facilitating promoter clearance, and creates a tunnel that surrounds the RNA transcript after it peels off a seven-base pair heteroduplex.” This involves seven subunits rotating 140 degrees and shifting 30 angstroms, then one subunit stretching out over twice its initial length. Then comes the grand finale:

“Perhaps the most unprecedented conformational change involves residues 160 to 190, which not only extensively refold, but move about 70 Å from one side of the polymerase to the other. This region refolds from a short helix and an extended loop into a pair of antiparallel helices (H1 and H2/3). The newly formed compact structure, named subdomain H, forms part of the RNA-transcript exit tunnel and contacts the 5' end of the RNA transcript on one surface and the nontemplate DNA on the opposite surface.”

The other end also undergoes shape-changes to create an exit tunnel for the RNA copy of the DNA. This “massive structural reorganization” of the protein machine causes it to form a protective tunnel, positively charged on the interior, in which the delicate work of translation can occur accurately. The tunnel interior melts the DNA into two strands, shunts the non-coding strand safely to the side, brings the RNA copy elements in and binds them to the DNA template. As the machine progresses down the track, it twists and bends the DNA against its natural inclination. This then supplies the energy to open up the strands and create a “transcription bubble” where the RNA letters (nucleotides) are mated with the DNA code in the “active site”. The tunnel has just the right shape to allow the RNA elements to come in. RNAP first has to attach to the DNA at a specific starting point called a promoter; this is the “initiation” phase. It appears that another protein called lysozyme regulates RNAP by binding to it, and preventing it from entering the “elongation phase” where all the gymnastics occur prior to the real translation work. In the initiation configuration, RNAP can produce only short chains (oligonucleotides) of RNA. The authors puzzle over whether there is a reason for this:

“One might ask why the abortive synthesis of short oligonucleotides exists and why the enzyme might not be “designed” to carry out the stable RNA synthesis that occurs in the elongation phase right from the start. The initiation of RNA synthesis at a particular site that is required for specific gene expression and regulation as well as the need for de novo, unprimed synthesis necessitates binding of the polymerase at a specific DNA location, the promoter. Furthermore, the binding of T7 RNAP to both the promoter and the downstream DNA appears to be essential for opening the bubble. Because short transcripts (2 to 4 nt) cannot form stable heteroduplexes, polymerase leaving the promoter prematurely would presumably lead to bubble closure and transcript displacement by the nontemplate strand. An enzyme locked in the elongation mode conformation seems unlikely to be capable of specific initiation and bubble opening. “

The authors also found that point mutations in certain spots either broke the machine or made it translate much less efficiently. Eukaryotes have additional protein parts in their translation machinery that do not require the contortions done by RNA Polymerase in these ultra-miniature life-forms.

Bacteria Borrowed Each Other’s Photosynthesis Technology 11/22/2002
How could bacteria evolve the complex processes of photosynthesis five times separately? By technology sharing. That’s a new idea propounded by a team at Dalhousie University in Nova Scotia, reports Elisabeth Pennisi in the Nov. 22 issue of Science. They didn’t have to invent it from scratch each time; they got the parts at the swap meet, via a process of lateral gene transfer.

Is Darwin’s Tree of Life Visible in the Genes? 11/26/2002
Two papers in the Proceedings of the National Academy of Sciences online preprints (11/25) complicate the task of deducing common ancestry from genetic codes. One by Kerry L. Shaw of University of Maryland is entitled, “Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets.” She concludes from her comparison of phylogenies built from nuclear and mitochondrial DNA that “speciation histories based on mtDNA alone can be extensively misleading.”

Another paper by three Penn State geneticists is called, “Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics.” They investigated the technique of Bayesian inference, a popular method for inferring causation, and found it too “liberal” compared to the more “conservative” bootstrap method. They write, “Bayesian analysis can be excessively liberal when concatenated gene sequences are used, whereas bootstrap probabilities in neighbor-joining and maximum likelihood analyses are generally slightly conservative. These results indicate that bootstrap probabilities are more suitable for assessing the reliability of phylogenetic trees than posterior probabilities and that the mammalian and plant phylogenies may not have been fully resolved.”

New Origin of Life Theory — Sans Primordial Soup – Turns Traditional View Upside Down 12/04/2002
In a press release, the Royal Society proclaimed a revolutionary new theory for the origin of life that “is set to cause a storm in the science world and has implications for the existence of life on other planets.” According to William Martin and Michael Russell, life did not begin in a warm little pond or primordial soup, but was incubated in iron sulfide rocks at the bottom of the sea. They believe this improves the odds that life will be found on other planets. Their hypothesis is to be published in the Jan. 2003 issue of Philosophical Transactions - Biological Sciences.

In the Dec. 2002 issue of the Royal Society’s Biological Proceedings, Krakauer and Sasaki introduce an unusual speculation about the origin of life. They argue, surprisingly, that randomness actually helped life develop. In their abstract, they have turned all the usual drawbacks into benefits :

“The origin of stable self-replicating molecules represents a fundamental obstacle to the origin of life. The low fidelity of primordial replicators places restrictions on the quantity of information encoded in a primitive nucleic acid alphabet. Further difficulties for the origin of life are the role of drift in small primordial populations, reducing the rate of fixation of superior replicators, and the hostile conditions increasing developmental noise. Thus, mutation, noise and drift are three different stochastic effects that are assumed to make the evolution of life improbable. Here we show, to the contrary, how noise present in hostile early environments can increase the probability of faithful replication, by amplifying selection in finite populations. Noise has negative consequences in infinite populations, whereas in finite populations, we observe a synergistic interaction among noise sources. Hence, two factors formerly considered inimical to the origin of life - developmental noise and drift in small populations - can in combination give rise to conditions favourable to robust replication.”

Molecular Motors — “Remarkable Machines” 12/17/2002
In a Commentary in the 12/16 online preprints of the Proceedings of the National Academy of Sciences, John Murray of University of Pennsylvania School of Medicine reviews what is known about molecular motors in the cell, particularly the linear motors (like trains on a track), which for all intents and purposes are true motors that actually move things and perform work that is measurable. Linear motors move along tracks (actin filaments or microtubules) in discrete steps of predetermined length (8nm for kinesin), and are polarized to move in only one direction; yet there are so many pairs of tracks and cars that the cell has no problem getting cargo to any point desired. Murray is especially intrigued by how motors like myosin and kinesin combine chemical process with mechanical actions in cycles that involve feedback between them; how do they do it?

“The details are still actively sought, but the overall process goes like this. One or more of the chemical transitions in the catalytic center causes a specific small movement of neighboring parts of the protein, and this small movement is mechanically amplified into a much larger movement of the core motor domain relative to the “tail.” Some of the chemical transitions also dramatically change the affinity of the head for the track. Conversely, binding of the head to the track alters the rates of some specific chemical transitions. Glossing over all of the uncertain bits, the net result (see Fig. 2) is that the head swivels its way along the track while ATP is hydrolyzed (i.e., in the entertaining but anatomically bizarre terminology of this field, the passive tail is pulled along by a wagging head)”
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Murray also finds it intriguing that many of the motors have two head domains. The two heads talk to each other constantly; neither can produce the motion by itself. In the case of kinesin, scientists are still trying to figure out whether the heads “walk” in a hand-over-hand fashion or move instead like an inchworm. He describes how “some motors work in groups, organized in ordered arrays of motors and tracks such as the interdigitating myosin and actin filaments of muscle tissue.” Yet other molecular motors work alone, shuttling their cargo on single tracks like handcars on a monorail.
The thrust of Murray’s commentary is hope that a new technique might help sort out the interaction of the two heads so scientists can discover how they work. In passing, he notes some of the performance specifications of these motors:

“In addition to processivity, other experimentally accessible parameters of a motor include its maximum velocity (~800 nm/s for kinesin; 5-50,000 nm/s for other motors), maximum force (~6 pN for kinesin; step size X force is limited by the energy of ATP hydrolysis, ~100 pN/nm per molecule, roughly 25 kT), maximum rate of ATP hydrolysis (~20/s per head for kinesin; 0.5-100/s for other motors), and affinity for tracks.”

By affinity for tracks, he means that these motors are attracted to the surface of the microtubules on which they zip around by forces of chemistry; like a wall climber with magnetic shoes, a kinesin can go 50-250 steps without falling off. The velocity measurements mean, in plain English, that these little motors are speed demons. Using his numbers and assuming a body length of 8nm for kinesin, if translated up to race car size, it would go 100 body-lengths per second; for a 12-foot race car, that’s over 800 mph. For the 50,000 nm/s motor, could it really be ... 400,000 mph?

Cell Chaperones: Did Generalists Evolve From Specialists? 12/30/2002
“Chaperones” are barrel-shaped protein machines in the cell whose task is to provide a safe folding place for newly-assembled polypeptides. One of their remarkable properties is the ability to help fold a wide range of proteins, something like a car wash that fits all models. Instead of the cell needing to maintain a specialist for each protein, a generalist does the job for most. In the Dec. 27 issue of Cell, researchers at Howard Hughes Medical Institute wrote up their experiment on “Directed Evolution of Substrate-Optimized GroEL/S Chaperonins.” They took a chaperone named GroEL/S and “evolved” it to do a better job at folding one protein named GFS, but found that as it got better at being a specialist, it got worse at being a generalist:

“These findings reveal a surprising plasticity of GroEL/S, which can be exploited to aid folding of recombinant proteins. Our studies also reveal a conflict between specialization and generalization of chaperonins as increased GFP folding comes at the expense of the ability of GroEL/S to fold its natural substrates.”

They feel this might help explain the evolution of these general-purpose folding stations: “Our results establish that the structure and reaction cycle of GroEL/S give it great plasticity, allowing the chaperonin to be tailored to increase the efficacy of folding of particular substrates.” Their champion GFP-folding specialist, however, lost in the all-around: “GFP-optimized chaperonins often led to significant growth defects.” Eukaryotes have a combination of generalist and specialist chaperones. The authors feel the conflict between efficiency and adaptability drives the evolution of these molecular machines. The authors note that proteasomes and nuclear pores are also generalists, but achieve their skill differently; for those structures, specialized “adapter proteins” bind to the substrate and then to the complex, something like tow bars specific to trucks, tractors, sedans and motorcycles first mating to their specific vehicle, allowing them to be all hooked to a common conveyor belt.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Orphans in the Genes: An Evolutionary Puzzle Is Growing 01/02/2003
Now that about 60 microbial genomes have been sequenced, a puzzle that was first brushed off as due to insufficient sampling is refusing to go away, and is getting worse. That’s the conclusion of two geneticists at Ben Gurion University, writing in the Jan. 2 issue of Structure. First, they explain what they mean by orphans:

“The genomes of most newly sequenced organisms contain a significant fraction of ORFs (open reading frames) that match no other sequence in the databases. We refer to these singleton ORFs as sequence ORFans. Because little can be learned about ORFans by homology, the origin and functions of ORFans remain a mystery. However, in this era of full genome sequencing, it seems that ORFans have been underemphasized.”

They explain the significance of ORFans to evolutionary theory in a series of unanswered questions :

“If proteins in different organisms have descended from common ancestral proteins by duplication and adaptive variation, why is it that so many today show no similarity to each other? Why is it that we do not find today any of the necessary “intermediate sequences” that must have given rise to these ORFans? Do most ORFans correspond to rapidly diverging proteins? If so, how rapidly do they diverge, and what are the forces involved in their rapid evolution? Is their rate of change constant or did the rapid changes occur only at specific times? Do these rapidly evolving ORFans correspond to nonessential proteins or to species determinants?”

It was thought that the numbers of ORFans would drop as more genomes were sequenced, because perhaps more data would provide more matches. With that hope, Siew and Fischer performed a detailed survey of the microbial genomes and graphed the trends. They found that 20% to 30% of sequences fall into the ORFan category. Even though each new genome reclassifies some ORFans as non-ORFans, the number of new ORFans grows faster than solutions. They predict 25,000 ORFans will remain when the 100th genome is sequenced. The authors examine possible explanations for the existence of these sequences of genetic material that are unique to each species. No appeals to sampling error or insufficient data appear to work; the phenomenon is real, and the problem is growing :

“We conclude that the increasing number of ORFans suggests that our knowledge of nature’s sequence diversity continues to grow, that ORFans may entail an intrinsic phenomenon in evolution, and that a global view of the protein world needs to consider the ORFan sequence families in addition to the large sequence families containing proteins conserved [i.e., unevolved] in numerous organisms.”

Their goal was not to explain the origin or function of ORFans, but to characterize the extent of the problem. Since each new published sequence is adding more ORFans than finding matches for them within known gene families, “Consequently,” they note, “the total number of ORFans is growing.”

Duplicate Genes: Fodder for Evolution, or Mechanism for Robustness? 01/02/2003
Genome sequences reveal a fairly large number of duplicate genes which show varying degrees of sequence similarity to one another. Susumo Ohno suggested 30 years ago that these might provide raw material for evolution; as useless copies, generated by chance during cell division, they might accumulate mutations that could be acted on by natural selection. Now, a paper by Zhenglong Gu et al in the Jan. 2 issue of Nature suggests instead that the duplicates provide robustness for the genome, allowing backup copies that can compensate for a DNA failure. In a News and Views analysis of the paper, Axel Meyer considers this a falsification of Ohno’s hypothesis, and wonders where raw material for evolution can now be found :

“All of this suggests that gene duplication provides a means of preserving function; even when two copies of a gene have diverged widely, they can still substitute for each other functionally to some degree. This, together with the fact that many genes and gene networks are similar in evolutionarily diverse species, hints that maybe Ohno was wrong after all. Are duplicated genes the stuff of developmental stability and of conservation of function rather than evolutionary innovation? If so, how did the diversity of life around us appear?”

He suggests some sources, like novel gene-regulatory sequences, but notes that evolutionary theory did not predict this :

“The discovery of many duplicated genes and parts of genomes has been an unexpected but interesting by-product of genome-sequencing projects. ... We are only now beginning to comprehend just how malleable genomes are, and also how resilient they are in the face of so much genetic perturbation; for instance, rearrangements and duplications of chromosomal segments are also commonplace. Gu et al have provided the first estimate (23-59%) of the contribution of duplicated genes to genetic robustness. This may be one reason why duplicated genes do not diverge to produce pseudogenes, or ‘die’, as quickly or as often as had been predicted on the basis of population-genetics theory.”

Molecular Rheostats Control Expression of Genes 01/10/2003
It’s not just the console; it’s the operators, say scientists, that deserve the award for technical excellence. In a Review article in the Jan. 10 issue of Cell, Richard Freiman of Howard Hughes Medical Institute and Robert Tijian of UC Berkeley use adjectives not normally found in dry scientific literature: elaborate, intricate, exquisite, and dramatic. They’re talking not about genes, but the systems that regulate them. A few examples :

• “The temporal and spatial control of gene expression is one of the most fundamental processes in biology, and we now realize that it encompasses many layers of complexity and intricate mechanisms.
• ... researchers have identified and partly characterized the elaborate molecular apparatus responsible for executing the control of gene expression.
• The molecular machinery responsible for controlling transcription by RNA polymerase II (RNA pol II) is considerably more complex than anyone had anticipated.
• Moreover, working out how subtle changes of the transcriptional machinery can vastly alter activation and repression in the context of the large battery of transcriptional initiation factors will be critical to understanding how elaborate gene expression patterns in metazoan organisms are orchestrated.
• The finding that posttranslational modification of Met4 by ubiquitin controls selective activation of one set of Met4-responsive genes and not another is remarkable and suggests that cells have evolved [sic] elaborate mechanisms to coordinately control gene expression but, at the same time, discriminate between different pathways by subtle mechanisms we have only begun to appreciate.
• It is not hard to envision that these lysine residues therefore serve as critical molecular switches that can respond to different signals in highly specific ways. In addition, since most proteins contain many lysine residues, transcription factors may undergo multiple modifications simultaneously or in sequential order, pointing to the possibility of generating complex networks of regulatory events.
• Clearly, transcription is exquisitely regulated in all organisms ... Future studies in diverse organisms and specialized regulatory pathways should further illuminate how transcription factor modification contributes to the elaborate mechanisms of gene regulation.

Freiman and Tijian note that gene number cannot be the sole determiner of the difference in outward body types between species, such as between a worm (19K) and a human (30K). There’s much more going on They estimate 10% of the genome is devoted to regulating the expression of genes, and that is largely responsible for the difference between you and the earthworm in your backyard:

“In other words, the dramatic phenotypic differences between a worm and a mammal can at least partially be rationalized by differences in the complexity of the regulatory code and not merely gene content. ... Regulation by modification not only enhances the functional potential of each individual transcription factor but also provides an effective means of greatly amplifying the functional plasticity of the transcriptional machinery required for combinatorial diversity. This quantum increase in the repertoire of regulatory events ultimately provides the rich tapestry of molecular interactions necessary to direct the diverse arrays of gene expression programs that define complex organisms.”

The transcription factors they describe in this paper (ubiquitination, sumoylation, acetylation and methylation) are in addition to the recently-recognized “histone code” system (see our November 4 headline about this), and may be even more vital :

While multiple covalent modifications of histone tails have been well characterized and shown to play a global role in gene expression ..., we postulate that modification of nonhistone regulatory proteins (i.e., transcription factors) will play an equally important and perhaps more specific role in directly modulating transcription.“

One particularly interesting aspect of their paper is that these regulatory programs, by working synergistically or antagonistically, can provide precision control comparable to a skilled audio technician’s hand on a mixing board: “We propose that potential cascades of modifications serve as molecular rheostats that fine-tune the control of transcription in diverse organisms.” So the regulation of gene expression, not merely gene number or content, may be the main factor that produces a navigating lobster, an archery-champion fish, a sonar-operating bat, or a catapulting horse.

Cell Contractors Take Delivery On Demand 01/13/2003
In a Review article in the latest issue of Current Biology, with the Ezekielesque title “Periodic Transcription: A Cycle Within a Cycle,” Linda L. Breeden discusses how cells optimize the time for transcribing genes into proteins. She opens with a picturesque construction analogy :

“If you were building a house, would it be better to take immediate delivery of every component required to complete the project, or to have things delivered as needed during the assembly process? From the point of view of efficient material management and the accuracy of the assembly process, the latter is the logical choice. Things needed continuously would be kept on hand throughout the process. Things needed only once, especially if they are not easily stored, would be delivered just before they are to be used. With a smaller inventory of things on hand, less time would be required to find things, less breakage would occur and fewer mistakes would be made as a result of mis-identifying parts with similar form but different functions. Given the logic of this strategy, it should be no surprise that it is frequently employed by cells. ... “

Breeden, who works at the Fred Hutchinson Cancer Research Center in Seattle, discusses recent findings that yeast and bacteria, and probably higher organisms, optimize their gene transcription in remarkable ways. The cell cycle refers to cell division; here is the cycle within the cycle :

“One remarkable feature shared by all the cell cycle-regulated transcription investigated to date is that each wave of transcription involves transcription factors that are also cell cycle-regulated at the transcript level. ... Some of these cell cycle-regulated transcription factors serve to induce the next wave of cell cycle-regulated transcription. Others serve as feedback regulators to extend, amplify or inhibit another wave of transcription. The result is a continuous cycle of interdependent waves of transcription wherein one wave can affect the timing, composition and/or persistence of an adjacent wave.”

These strategies serve to control transcript complexity during the cell cycle. Breeden concludes :

“Logic dictates that reducing the complexity of transcripts at any given time during the cell duplication process would improve its fidelity and efficiency. ... What is clear is that both bacteria and yeast have invested considerable effort into doing just that. The transcriptional circuitry that has evolved [sic] is a series of consecutive and interdependent waves of transcription driven by transcription factors that are themselves cell cycle regulated. It is a simple, yet flexible strategy, with many opportunities for signaling inputs from external sources. Feedback loops have been incorporated which appear to coordinate critical events, and may buffer the cell cycle when conditions change. There are clearly gaps in our understanding, but there is no doubt that this is a general strategy that underlies the yeast and bacterial cell cycles and there is tantalizing evidence that the same may be true in higher cells as well.”

She leaves it unexplained how these strategies evolved, other than to note that they appear to be conserved from bacteria upwards. “If it’s conserved,” she says, “there’s usually a good reason.”

Bacterial Cytoskeleton Is a Plastering Artist 01/16/2003
You learned in school that bacteria don’t have a cytoskeleton. Wrong. Like eukaryotes and all higher organisms, they have internal “cables” but they are not made of actin, but a protein named Mbl. The Oxford team that found this out in 2001 (see Science News) has now found out something even more amazing. Using time-lapse photography and fluorescent dyes, they found that the cables are dynamic structures. They assume a helical shape from one end of the bacterium to the other, and rotate against the inside of the cell wall. Carballido-Lopez and Errington et al, writing in the Jan. 14 issue of Developmental Cell, think they know what they might be doing. They might be plastering layers of material on the inner side of the cell wall. As the cables rotate and the material deposited stretches in the opposite direction, the result is a “multilayered fabric composed of layers of material, each of which is inserted at an angle to the previous overlying layer ... the resultant meshwork structure should be more resistant to shearing forces than a structure in which the stress bearing fibers are inserted in a highly parallel manner.” They are currently testing this model. The fibers, made of peptidoglycan, work their way to the surface and are discarded. The rotating cables inside the organism, therefore, constantly replenish the cell wall from the inside. Cell division is able to operate because the cables are continually remodeled in about 8 minutes on average.
DNA After 50 Years Continues to Astound Biologists 01/27/2003
To celebrate the 50th year of Watson and Crick’s (and Rosalind Franklin’s) discovery of the structure of DNA, the Jan. 23 issue of Nature has a special section entitled, “The Double Helix – 50 Years.” It contains 16 articles by scientists and historians, looking backward and forward, on what we’ve learned so far and what prospects lie ahead.
In short, DNA is far more complex than the simple double helix we all know from pictures, and there is much we still have to learn. A common theme is that DNA is not a simple, static library, but a very dynamic system, constantly in motion, surrounded by a much more dynamic and complicated set of protein translators, protectors, repairers, and regulators. Words like elegant, exquisite, and marvelous festoon the word parade celebrating “this miraculous molecule” as Helen Pearson calls it in her introductory editorial.
Philip Ball in “Portrait of a Molecule” describes the incredibly dense packaging process that telescopes 1.8 meters of the DNA ladder into six micrometers of space – a packing ratio of 7,000 to one. Somehow in all the commotion of transcription and cell division, it maintains a “structured chaos” in the nucleus: “It is a constantly changing structure, but not randomly: there is method in there somewhere,” he says, revealing how much remains to be learned. After dazzling the reader with descriptions of the winding, packing, coiling, and supercoiling processes that DNA undergoes in its dizzying dance, he concludes :

“If all of this destroys the pretty illusion created by the iconic model of Watson and Crick, it surely also opens up a much richer panorama. The fundamental mechanism of information transfer in nucleic acids - complementary base pairing - is so elegant that it risks blinding us to the awesome sophistication of the total process. These molecules do not simply wander up to one another and start talking. They must first be designated for that task, and must then file applications at various higher levels before permission is granted, forming a complex regulatory network .... For those who would like to control these processes, and those who seek to mimic them in artificial systems, the message is that the biological mesoscale [i.e., between molecules and organelles], far from being a regime where order and simplicity descend into unpredictable chaos, has its own structures, logic, rules and regulatory mechanisms. This is the next frontier at which we will unfold the continuing story of how DNA works.”

Bruce Alberts, President of the National Academy of Sciences, in “DNA replication and recombination”, repeats a theme he has expressed for years, that DNA-protein complexes are best described as interacting molecular machines (a word he uses over a dozen times). He asks how precise these machines have to be :

“For the first 30 years after Watson and Crick’s discovery, most researchers seemed to hold the view that cell processes could be sloppy. This view was encouraged by knowledge of the tremendous speed of movements at the molecular level ....
Quite to the contrary, molecular biologists now recognize that evolution has selected for highly ordered systems. Thus, for example, not only are the parts of the replication machinery held together in precise alignments to optimize their mutual interactions, but energy-driven changes in protein conformations are used to generate coordinated movements. This ensures that each of the successive steps in a complex process like DNA replication is closely coordinated with the next one. The result is an assembly that can be viewed as a ‘protein machine’. ... And DNA replication is by no means unique. We now believe that nearly every biological process is catalysed by a set of ten or more spatially positioned, interacting proteins that undergo highly ordered movements in a machine-like assembly.”

The simple 2D cartoon models of DNA have to go, Alberts concludes; “because most biological subsystems have turned out to be far too complex for their details to be predicted. ... For this reason, we urgently need to rethink the education that we are providing to the next generation of biological scientists.”

DNA Damage Repair Team Hears Alarm at a Distance 01/30/2003
DNA, like a ladder, can break, and when both sides break, it’s serious trouble. Cancer and other lethal diseases can result from these double-stranded breaks, or DSBs, which are “the most deadly” of DNA failures. Most of the time, fortunately, there is a response system called ATM that knows just what to do. It can repair both sides of a broken DNA molecule, quickly and efficiently; when not possible, ATM knows how to throw the self-destruct switch to kill the cell so it won’t become cancerous or otherwise dangerous.
There are many DNA repair mechanisms for many kinds of problems, but most are active during cell division, when there is the highest likelihood for error. ATM, by contrast, works in the resting phase. The heart of the system is a pair of “giant” proteins, normally “locked together in a tight embrace that prevents them from forming any promiscuous liaisons with other proteins” – i.e., their mutual hammerlock keeps them from fraternizing till duty calls. A DSB crisis triggers an alarm; the ATM response separates the repairmen by a process called autophosphorylation, which activates them and puts them to work.
Christopher Bakkenist and Michael Kastan of St. Jude Children’s Hospital in Memphis, Tennessee, writing in the Jan. 30 issue of Nature, found, to their amazement, that ATM can detect the signal some distance away from the problem. A double-stranded break occurring deep within chromatin-wrapped bundle of DNA can get help fast, even if the repairmen are not near. How does ATM differentiate a real crisis from the normal frenzied activity of cell division, transcription, and translation? Danish cell biologists Bartek and Lukas are amazed at the sensitivity of this emergency response system :

“Finally, the sensitivity, extent and speed of the ATM response are truly astonishing. Doses of irradiation that cause only a few DSBs in a human cell activate the majority of ATM within minutes. And induction of just two DSBs per cell is enough to induce the crucial ‘autophosphorylation’ of ATM.”

Much remains to be learned about this paramedic team, but one thing is clear: it keeps us alive. “Our genetic blueprint is constantly assaulted by adverse environmental and cellular influences, such as ultraviolet or ionizing radiation and various chemicals,“ write Bartek and Lukas. “Fortunately, these massive attacks on our DNA are largely counterbalanced by promptly deployed, multifaceted surveillance and rescue operations.”

Your Electric Personality 02/05/2003
You shine like a 116-watt light bulb, and run 522 amps of electrical current. To run your power plant, three sextillion protons per second are continually being pumped across enough super-thin membrane, filled with embedded generators, to stretch over three football fields. These and other amazing facts are described by Peter Rich in a Concepts article about mitochondria (our miniature power plants) entitled “Chemiosmotic coupling: The cost of living” in the Feb. 5 issue of Nature.
He recalls Peter Mitchell’s controversial work in the 1960s that first suggested biological electron transfer was linked to ATP synthesis – a discovery that won him the Nobel Prize. Since then, interest in mitochondria switched on, and increasing knowledge about its electrical activities has lit up the imagination. Here’s part of Peter Rich’s technical description (bracketed notes added):

“An average human at rest has a power requirement of roughly 100 kilocalories (420 kilojoules) per hour, which is equivalent to a power requirement of 116 watts - slightly more than that of a standard household lightbulb. But, from a biochemical point of view, this requirement places a staggering power demand on our mitochondria. Mitchell’s work showed that the electrochemical gradient of protons across the inner mitochondrial membrane that drives ATP synthesis is roughly 200 mV, and most of this is the electric field component.

If it is assumed that 90% of human power is provided by the protons that are transferred through the ATP synthase, then the transmembrane proton flux would have to represent a current of 522 amps, or roughly 3 x 10exp21 protons per second. ... Assuming a conversion efficiency that is close to unity [i.e., 100% efficiency], ATP is reformed at a rate of around 9 x 1020 molecules per second, equivalent to a turnover rate of ATP of 65 kg [143 lb.] per day and with much higher rates than this during periods of activity. This output is itself powered by the oxygen-consuming respiratory chain.

A typical adult male consumes around 380 litres of oxygen each day, and top athletes can sustain rates that are ten times greater for limited periods. Most (90%) of this oxygen is reduced to water by the terminal respiratory-chain enzyme, cytochrome oxidase. The inner mitochondrial membrane contains around 0.4 nanomoles of this enzyme per milligram of protein. It can work at a rate in excess of 300 electrons every second, but probably operates at an average rate of no more than 50 per second. Hence, an average human will need 2 x 10exp19 molecules [20 quintillion] of cytochrome oxidase to support oxygen consumption. With the inner mitochondrial membrane having a lipid/protein weight ratio of 1:1, the cytochrome oxidase would be associated with about 70 ml of lipoprotein membrane. However, the membrane’s thickness - only 6 nm [6 billionths of an inch] - means that the surface area of the inner mitochondrial membrane in an average human would be around 14,000 m2.”

Rich, biologist at University College, London, is focused not so much on the wonders of the system but the “cost of living” – the “herculean task” that eukaryotes undergo to synthesize ATP for energy consumption, through a membrane that acts as a capacitor, and ATP synthase rotary motors that take the protons and make ATP from ADP and phosphate. “The energy thus stored,” he explains, “can be released by ATP hydrolysis, a reaction that is used by the myriad energy-requiring enzymes that maintain cellular function.” He points out that mutations or defects in the mitochondrial DNA are implicated in physiological disorders, and probably increase throughout our lifetimes. So as we age, our light bulbs eventually burn out.

Scientists Pump the Flagellum Engine 02/10/2003
Japanese researchers have found that flagella, the whiplike propellers that make bacteria swim, can get flooded with too many protons if the pH is lowered inside, reports Nature Science Update. Like a flooded car engine, the motors come to a stop. But they can run fine again if the artificially-induced pH change is reversed. The article concludes by discussing the functional specifications of these molecular machines:

“This is a motor with quite remarkable properties,” says Robert Macnab of Yale University in New Haven, Connecticut, who studies the assembly of bacterial motors. “It runs like a battery, moves like a ship’s propeller, has a gear switch so it can rotate in either direction, and it’s under the control of information from [the] environment. These are biological functions at their most simplified form, and yet there are 60 different types of components in this little engine.”

Kendall Powell explains the interest in these motors: “Researchers are keen to understand such chemically driven biological motors, which are only millionths of a millimetre across, as electronics do not work on this scale.”

Protein Machine Does Gymnastics 02/13/2003
Scientists are bringing into sharper focus an amazing molecular motor named dynein. Dynein is responsible for much of the movement in the cell: the whiplike action of sperm tails, the sweeping action of cilia, and the ferrying of cargo down the microtubule intracellular railroad. The UK research team of Stan Burgess et al in the Feb. 13 issue of Nature imaged thousands of the little molecules (large by protein standards, with a molecular mass of over 500,000) that work something like railroad handcars. They have a ring-shaped hexagonal head of six AAA proteins to which is added a C-terminal domain. Emerging out of one side and in the same plane as the ring is a stalk, which has a structure on the end that attaches to the microtubule. Emerging out the other end is a stem that attaches to whatever cargo needs to be transported. The stem is fastened to the ring by a linker, that seems to act like a ratchet on a gear during the cycle.
How does it work? Though the details are still fuzzy, it appears that ATP hydrolysis occurs in the central ring, or head domain; i.e., energy is extracted from ATP, producing ADP and phosphate, putting the machine into a “cocked” state. This causes a conformational change (parts moving in relation to one another) resulting in a 34o rotation of the ring relative to the linker. The head domain rolls in relation to the stem, producing mechanical spring energy. Since the stalk and stem have some flexibility, they are “capable of storing elastic strain energy when the molecule develops force against a load.” The movement pops out the ADP, and then the mechanism springs back to its cocked position; the so-called “power stroke.” Simultaneously, another ATP energy pellet enters the engine for the next cycle.
The angle between the stalk and stem thus changes back and forth in a rocking fashion, producing mechanical leverage, as the linker continually engages and disengages in the central ring, like a hook catch on a gear. As a result, the dynein motor slides down the microtubule monorail in 15-nanometer jumps. But that’s not all; there is two-way communication between the tip of the stalk and the engine in the head, and even more amazing regulatory mechanisms that tell the motor where and how fast to go.
In their News and Views write-up on the paper, entitled “Molecular motors: A magnificent machine,” Richard B. Vallee and Peter Höök consider this a remarkable gymnastic ability that is rarely seen in motor proteins. The dynein machines actually use the chemical energy stored in ATP to produce force and carry out work. They point out that this action occurs many times per second in the molecular motor.
If you can’t reach the Nature article, the BBC News has a summary of it that likens dynein to engines with pistons that make wheels turn. One of the researchers is quoted likening the system to a railway network: “Our body is full of proteins which form tracks. Along these tracks, molecular motors are the locomotives, transporting a variety of cargoes to wherever they are needed”

Cell Nucleus More Than Just a Bag of Chromosomes 02/19/2003
Scientists at Johns Hopkins Medical Institutions are finding that the nucleus of the cell is not just a passive storage area for genetic information. Kathy Wilson told the AAAS meeting on the 17th that the nucleus is “is really the cell’s mothership, a crucial and very active source of information, support and control.” One amazing feat occurs during cell division. Chromosomes are pulled apart outside of the nucleus, so the nucleus must disappear during the process. It does not just fall apart. Wilson described it as “an orchestrated process similar to the pulling apart of the chromosomes. It seems to involve the same structures and the same tiny motors. It’s almost a practice run for moving the chromosomes”

Cell Repairs its RNA, Too 02/20/2003
The cell has elaborate ways to safeguard its genetic library by repairing DNA, but now scientists are finding the same enzymes can also repair RNA. In the Feb. 20 issue of Nature, Begley and Samson of MIT discuss the findings of Aas et al that RNA methylation damage can be repaired by the same AlkB enzyme that repairs DNA. This is surprising because RNA and proteins were considered more expendable than DNA, but they explain why it makes sense :

“Why, though, should it be necessary to repair damaged RNA? The answer could be that although DNA is the final arbiter of genetic information, RNA is essential for the most basic biological processes. RNA-based primer sequences are required for DNA replication; and mRNAs, transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) are all needed during the elaborate process of protein synthesis. Even the formation of peptide bonds by ribosomes (the cell’s protein-making machines) turns out to require catalysis mediated by rRNAs. Moreover, a battery of small, non-protein-coding RNAs regulates a variety of other cellular processes.”

So maintaining RNA integrity is important for proper cellular function. And repairing damaged RNA may be more efficient than destroying it and starting again. Ribosome assembly is a complex, energy-intensive process, and it is not hard to imagine that the thrifty repair of damaged rRNA would be preferable to disassembling or discarding an entire ribosomal particle.

Another surprise is that the repair mechanism seems to be able to distinguish between DNA and RNA, and between toxic methylation damage and normal biological methyl groups attached to some RNAs. Begley and Samson think it not unlikely that DNA and RNA might overlap in other ways, such as in cell signalling. Update 06/16/2003: In the June 17 issue of Current Biology, Alfonso Bellacosa and Eric G. Moss from the Fox Chase Cancer Center in Philadelphia remind us that “RNA in a cell is subject to many of the same insults as DNA“ and that “the ‘information content’ of cellular RNA is greater than that of the chromosomal DNA” because almost all of RNA’s sequences have functional significance (messenger RNA and transfer RNA), whereas only 3% of the DNA has coding potential. Since RNA shows significant response to anticancer agents, the authors suppose that newly-discovered RNA repair pathways are important for preventing cancer:

“A cell has a great investment in its RNAs – they are working copies of its genomic information. The study of mRNA biogenesis in the last few years has revealed an elaborate surveillance mechanism involving factors such as the UPF proteins that culls aberrantly spliced mRNAs and mRNAs with premature termination codons. There might be a hint that such RNA quality control mechanisms go awry in cancers, just as DNA quality control mechanisms do, where aberrantly spliced transcripts accumulate in a tumor. Now that the gates are open, we may have a flood of studies on the RNome [the RNA genome] stability and cancer.”

Another Rotary Motor Found in Cells 02/24/2003
Another member of the ATPase (ATP synthase) superfamily has been shown to rotate and produce three ATP per cycle. The well-known FoF1-ATP synthase was imaged in rotation about five years ago. Another enzyme, VoV1-ATPase, was known to be structurally similar and has been assumed to rotate also, but experimental evidence was lacking. The Japanese have done it again. They attached a bead to the stalk and imaged the tiny molecular machine rotating counterclockwise at about 144 rpm, which they assume is the natural rotation rate without the bead attached.
VoV1-ATPase is responsible for acidification of eukaryotic intracellular compartments and ATP synthesis in Archaea and some eubacteria. FoF1-ATP synthase resides in the mitochondria and chloroplasts; VoV1-ATPase is embedded in various intracellular acidic compartments. This enzyme’s D subunit acts like a rotor shaft, analogous to the gamma subunit of F1ATPase. The experimental results are written up in the Proceedings of the National Academy of Sciences online preprints for Feb. 21.
How they work: The Fo and Vo subunits of the machines are embedded in the membranes and use proton motive force to rotate. The F1 and V1 subunits are where ATP synthesis takes place. They contain six lobes that are acted on by a rotor shaft, or camshaft, attached to the rotating portion. The six lobes come in pairs. As the camshaft turns, it causes each pair to cycle through the manufacturing steps: load the ingredients (ADP and phosphate), squeeze them together into ATP, then eject the ATP into the surrounding medium. Each pair is undergoing one of these stages every 120o turn of the camshaft, so that 3 ATP are produced for every full turn. ATP is the energy currency used by most processes in the cell. On a busy day, your miniature motors can recycle an amount of ATP equal to or exceeding your body weight.

Your Model Train Set 02/25/2003
Model train enthusiasts never had it so good. Imagine five different models of finely-crafted engines, all in perfect working order, and enough track to cover a city. That’s what each of us has, right now, inside our cells. But don’t feel top dog; even lowly bacteria have them, too. To prove we’re not making this up, read “The Molecular Motor Toolbox,” a Review article in the current issue of the journal Cell, by Ronald D. Vale of the Howard Hughes Medical Institute. He begins:

“A cell, like a metropolitan city, must organize its bustling community of macromolecules. Setting meeting points and establishing the timing of transactions are of fundamental importance for cell behavior. The high degree of spatial/temporal organization of molecules and organelles within cells is made possible by protein machines that transport components to various destinations within the cytoplasm.”

Vale reviews the five major motor engine families that ferry cargo around the cell: actin, dynein, conventional homodimeric kinesin, heterotrimeric kinesin II, and Unc104/KIF1. These engines show remarkable flexibility and diversity in living things, from plants to sea squirts to fungi to worms, and are highly conserved from the smallest organisms to the largest. What about the switching? What keeps the engines from colliding on the tracks?

“To achieve law and order on the intracellular highways, the multiple cargo-carrying motors in a single cell must be regulated. In the majority of animal cells, individual organelles switch frequently between anterograde (microtubule plus-end-directed) and retrograde (minus-end-directed) movement .... In most cells, relatively little is known about the regulation and coordination of bidirectional motion. ... individual cargoes move primarily unidirectionally in these extended processes, and a switch in direction occurs when cargoes reach the ends of these elongated structures.”

There is an unknown switching mechanism at so-called “turnaround zones” on the microtubules that dynein and kinesin engines travel on.

“The microscopic observations of cargo transport in axons and flagella raise a number of similar questions. How do the opposite polarity motors, kinesin and dynein, coordinate their activities? What kind of machinery processes the incoming cargo and switches motor direction at the ‘turnaround’ zones? Molecular answers to these questions are beginning to emerge but are far from complete.”

As a sidelight, another review article in the same issue of Cell by a team from UC San Diego describes how these motors are involved in tugging the chromosomes apart during cell division (mitosis). In fact, the whole Feb. 21 issue is a good source for current knowledge about the cell’s inner workings: mitochondria, cell division, signalling, transport, etc. But back to our story.
Vale points to fascinating indications that the motors signal each other and coordinate their actions. After discussing some of these possibilities, he concludes, “Fifteen years ago, only a few molecular motors were known. In contrast, complete inventories of molecular motors are now available in a number of diverse organisms. While these remarkable accomplishments have answered many questions, the genomic inventories also have exposed many areas of ignorance.” Well, back to the lab; gotta get to “work.” Biochemistry can be fun. You get to play with miniature railroads.Nature Science Update reports that NASA engineers are studying the intracellular railroad for spacecraft ideas. UCLA got a $30 million NASA grant to begin the Institute for Cell Mimetic Space Exploration, whose mission is to “come up with biology-inspired devices that could facilitate space travel 30 years from now.” Some of the plans include imitating actin.

Footnote: In the same issue of Cell, an Austrian team discusses the state of knowledge about meiosis (cell division for sexual reproduction). They note that there is no evidence for evolution of this highly complex series of processes :

“In summary, the behavior of chromosomes in meiosis is much more complex than in mitosis. Additional demands such as chiasmata formation, mono-orientation of sister kinetochores, protection of centromeric cohesion, and prevention of DNA replication between the two divisions are imposed upon the chromosome segregation machinery. These processes are discussed in detail in the following sections. Despite its greater complexity, there is no clear evidence that meiosis evolved later than mitosis. There are, for example, no extant lineages that appear to have split off the eukaryotic tree before the evolution of meiosis (Cavalier-Smith, 2002).”

Footnote 2: Another molecular motor story appeared on EurekAlert Feb 25. Stanford scientists are studying kinesin, the “workhorse of the cell,“ which hauls chromosomes, neurotransmitters and other vital cargo. Joshua Shaevitz describes it: “This is one of the most efficient engines anyone has ever seen. Some estimates put it at near 100 percent efficiency. It’s an amazing little thing.” His colleague Charles Asbury chimes in with elegant prose, “Kinesin is an example where Mother Nature kicks our butt. For me, I’m motivated just by understanding how this fascinating thing works.”

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Gatekeepers of the Cell Nucleus Revealed 03/04/2003
Five thousand gates control access in and out of the cell nucleus: the Nuclear Pore Complexes (NPCs). In the March 4 issue of Current Biology, two Canadian biochemists survey what is known about them. On a molecular scale, they are huge assemblages with many parts, made up of 30 different types of proteins. But these are not just holes in the nucleus; they are departments of homeland security. Squads of other proteins scan the visitors and badge them if authorized so that they can run the gauntlet. And that’s not all. Now evidence is growing that the NPC, through its power to control what enters and exits the nucleus, is a regulator of gene expression. The authors say that eukaryotes (that’s us and other multicellular organisms) have the “Cadillac” model NPC composed of 125 million atomic mass units; single-cell organisms like yeast, with 50 million, have the “sportier” version.

Ready-Mix Patch Kit Stands Ready To Repair Your Body’s Brick Walls 03/19/2003
You’ve probably used those packets with two compartments that do something when the dividing membrane is broken, allowing the components to mix: instant heat, instant cold, instant glue, or instant light. Your body has something like that to repair its tissues. Tissues are the webs of specialized cells that distinguish us multicellular organisms from the rest, and the bulk of tissues are composed of epithelium. Epithelial cells line up in tightly-knit ranks forming the lining of most organs, the lungs and windpipe, the digestive tract, and the skin. Because they are subject to injury, these membranes must have a means of repairing themselves quickly. So they have a kind of ready-mix patch that works only when two components combine. But the system must work flawlessly, or a disaster can result.

Keith Mostov and Mirjam Zegers talk about this in the Mar. 20 issue of Nature, “Cell Biology: Just Mix and Patch,” reporting on work by Paola Vermeer and company in the same issue. Epithelial cells have two linings. Consider the respiratory tract as an example. One lining, the apical side, faces the airway. The other, the basolateral side, lines the other end and the neighboring cells. These two linings are segregated by a kind of O-ring seal that makes a tight fit between neighboring cells. Scientists recently found that the basolateral membrane has one component of the patch, called erbB2, and the apical side has a matching component called heregulin. Normally kept apart, they can be brought in contact when a breach occurs in the epithelial tissue. Together, they activate a complex series of steps leading to cell division and presto! the gap is filled in with another snug-fitting cell, and life goes on. It is essential these active ingredients don’t mix at the wrong time. Too much cell division and you know what happens — cancer. Science Now has a news write-up on this story, and its discovery that is “so beautifully simple.”

A few more Cool Cell Tricks were reported recently:

• Cells have an exquisite toolkit for dealing with iron. Three New Zealand scientists writing a Perspective special feature in the Proceedings of the National Academy of Sciences describe a family of proteins called transferrins that clamp around iron and delicately transport this very toxic atom to wherever it’s needed in the cell. The clamp has a hinge that opens the structure and disgorges the iron when it is safe to do so. Another protein called hemopexin transports heme by holding it in the center of a four-part structure.
• Another Special Feature in the same issue talks about nitrogenase, which we discussed Sept. 6, 2002. Two Harvard chemists attack this puzzling molecule with the zeal of Captain Ahab pursuing Moby Dick (this is actually how they end their article), but in spite of the best efforts of scientists for decades, “Few problems in bioinorganic chemistry have proved as challenging and refractory.” They speak of techniques this molecule uses that are “biologically and chemically unprecedented,” and marvel like Scotty and Captain Kirk aboard an alien ship trying to figure out a novel dilithium crystal reactor. Hidden inside the inner sanctum of this molecular machine is a secret method for separating nitrogen atoms at room temperature that is the dream of agricultural chemists, because artificial nitrogen fixation (e.g., fertilizer making) is costly and energy intensive. “The synthetic problem of nitrogenase, nevertheless, remains unsolved,” but they think we’re getting warmer.
• Current Biology for March 18 has a quick guide to a very versatile gene called APC (adenomatous polyposis coli), without which we either die or get colon cancer. It moves all over the cell, in and out of the nucleus, even riding the intracellular railroad. APC has many jobs. It’s a potent tumor suppressor, it regulates gene transcription, and it has a role in “maintaining adherens junctions, and also helps to tether mitotic spindles to the cortex and to orient them in the epithelial plane. In mammalian cells, APC has been implicated in cell migration. APC also helps safeguard the fidelity of chromosome segregation in mitotic cells.”

DNA Repairmen Can Back Each Other Up 03/21/2003
The DNA Damage Response team has many specialized technicians, but now scientists have found some of them can fill in for a fallen comrade. Amundsen and Smith of the Fred Hutchinson Cancer Research Center, writing in the March 21 issue of Cell first set the stage for the story:

“Faithful repair of broken or damaged DNA occurs by homologous recombination. This process requires a series of enzymes, collectively forming a “recombination machine,” that act on broken DNA. At least three broad classes of activities—helicases, nucleases, and synapsis proteins—constitute parts of this machine and can be provided either by one complex protein or by several separate proteins.”

They describe two team members, RecBCD and RecF, that act independently under normal conditions. “But recent analysis of an E. coli mutant that lacks RecBCD nuclease activity,” they announce, “normally required for that pathway of recombination, provides a striking example of how functional parts from these two recombination machines can be interchanged.”

Their minireview entitled, “Interchangeable Parts of the Escherichia coli Recombination Machinery,” also describes how the machines work. They feel this is probably not an isolated example of interchangeable roles: “Perhaps in wild-type cells also, there are situations of altered DNA metabolism not yet recognized in which activities from the two recombination machines interchange to maintain chromosomal integrity.”

Deep Inside You, Machines Climb Monkey Bars 03/28/2003
“Within every neuron is a vast protein trail system traversed by a small protein engine called Myosin V,” begins a press release from University of Pennsylvania Health System. But these trails, made of actin, are more like monorails than country paths. For a long time, biophysicists have wondered how myosin V moves along the monorail. How does this little motorcar ride the rail without losing its grip? They know it has two heads that grip the rail, and a tail that holds the cargo. Do the heads (actually more like feet) slide along like an inchworm, or move hand-over-hand? Now at long last, Yale E. Goldman’s team thinks they have solved it. The tiny molecular motors move hand over hand, much like kids in a playground. Goldman explains: “It turns out that myosin tilts as it steps along the actin track – one head attaches to the track and then the molecule rotates allowing the other head to attach – much like a child on a playground crosses the monkey-bars hand-over-hand.” How did they see it? “Using single-molecule fluorescence polarization, we could detect the three-dimensional orientation of myosin V tilting back and forth between two well-defined angles as it teetered along.”

Molecular Motors: Plants Have Sewing Machines 03/31/2003
In a discovery that “represents a previously unreported concept and will stimulate further research,” three German biologists have reported that plants have a molecular motor that acts like a sewing machine. Schleiff, Jeilic and Soll of Munich studied an unusually large GTP-binding protein named Toc159 that was previously thought to be just a passive receptor on the surface of the chloroplast. Their analysis shows that “Toc159 acts as a GTP-driven motor in a sewing-machine-like mechanism.”
They explain that “The translocation of proteins across cellular membranes is a key mechanistic problem for every cell.” Apparently, Toc159 threads its needle by grabbing a precursor protein (preprotein) of the protein needing to get through the membrane. Then, Toc159 empowered by GTP actually pushes the cargo through the Toc75 channel, which expands to accommodate the thread-like protein. Once the cargo is through, Toc159 resumes its position. “Through multiple rounds of preprotein binding and GTP hydrolysis,” the authors explain, “Toc159 will push the polypeptide across the membrane.” Thus it works in a rocking fashion, sending the threads of protein through pores in the cloth of the chloroplast membrane, with two conformational changes and two expenditures of GTP to GDP for each cycle. They suspect other examples of this motor mechanism will be found.
Source: “A GTP-driven motor moves proteins across the outer envelope of chloroplasts,” in the Proceedings of the National Academy of Sciences online preprints, 3/28/03.

Fail-Safe Mechanism Protects Against Gene Re-replication 04/09/2003
As if you didn’t already have enough to worry about: some 8 million of your cells are dividing at any one time, and they had better get it right, each and every time, because mistakes can be disastrous. During the cell division process (the cell cycle), all those DNA base pairs need to be duplicated so that each daughter cell has a copy. How does the cell guarantee no strand is accidentally copied twice? The cell has a system of checks and balances. A stretch of DNA needs to first obtain a license to be copied. Once the copy is done, the license is removed. Writing in the April 4 issue of Cell, Scottish biologist J. Julian Blow explains how this works:

“The replication of eukaryotic chromosomal DNA requires the initiation of replication forks from thousands of replication origins. These must be regulated so that none fires more than once in each cell cycle. The cell achieves this by breaking the initiation process into two nonoverlapping phases. In the first phase, occurring in late mitosis and early G1, replication origins are ‘licensed’ for replication by assembly of a prereplicative complex (pre-RC) of initiation proteins. When replication forks are initiated at licensed replication origins during the subsequent S phase, the pre-RC is disassembled, converting the origin to the unlicensed state incapable of supporting further initiation. In order for this system to work properly, the licensing system that assembles new pre-RCs must shut down before S phase starts.”

He reports on a new function of a multi-talented protein named Ran that is involved in this last step. But it is probably far from the whole story. Blow concludes, “it is unlikely that direct inhibition of licensing by Ran-GTP is the only control. Previous work suggests that several redundant mechanisms might exist to minimize the risk of re-replication occurring, an event with potentially catastrophic consequences.” The Preview article is entitled, “A New Role for Ran in Ensuring Precise Duplication of Chromosomal DNA.”

DNA Epic Saga a Bigger Production than First Realized 04/12/2003
“DNA’s Cast of Thousands” is the subject of Elisabeth Pennisi’s commentary in the April 11 issue of Science special issue on “Building on the DNA Revolution.” She recounts the history of the discovery of DNA, and where research is headed. The story line is one of increasing complexity: nucleic acids (1860), a blurry idea of a helical molecule (1951), the genetic code deciphered (1953), then a mushrooming bonanza of discoveries about supporting cast: messenger RNA, transfer RNA, transcription factors, polymerases, repair teams, histones, chromatin, and more. Typical quote: “Again, the process is proving to be even more complicated than researchers initially realized.” Pennisi ends on the recent suggestion that a histone code exists that is “as complex and important as the DNA code.” She ends, “Forty years ago, Brenner and others were convinced that the central questions in molecular biology would be answered well before the turn of the century. Now they know better. The nature of the histone code is just one of many problems whose complexities are left to be unraveled.”

Traffic Controls in the Cell Prevent Traffic Jams 04/14/2003
Cells have a variety of cargos that need shipping, including messenger RNA particles, mitochondria, endosomes, lipid droplets, and more. These are continually on the move in the cell, going from one part of the cell to another, where needed. They are carried along by molecular motors that move along tracks called microtubules that have a + (plus) end and a - (minus) end. Each transporter moves toward its specific polarity: kinesin moves toward plus, and dynein moves toward minus. Both motors can grab a piece of cargo simultaneously, but this creates a situation like a boxcar being pulled by engines facing opposite directions. How does the cell coordinate the movements? Is it a tug-o'war, or is there some switching action that coordinates the traffic?
Apparently the latter. In the April 15 issue of Current Biology, Steven P. Gross of UC Irvine reviews today’s understanding on the subject. Although much remains to be explained, a complex of proteins appears to act like springs to engage or disengage the transporter when necessary, as if putting the idle engine in neutral so the driving engine can have priority. In addition, additional regulation is needed to govern which direction has priority. The result is that even with one-way engines, interference is avoided, so that cargo can move both forward and backward on the track, and even reverse direction if the need arises. By removing these controls, scientists have been able to create traffic jams and pile-ups in a system that otherwise works in smooth coordination.

Cell Celebrated 04/17/2003
The April 17 issue of Nature features a collection of reviews on cellular dynamics: cell division, the cytoskeleton, microtubules as molecular machines, molecular motors, and more. In the overview article, Thomas D. Pollard of Yale sees this all as the triumph of the reductionist agenda: i.e., that all this complexity can be explained from simple evolutionary precursors.

How the Cell Avoids Typos 04/29/2003
Some of the most intriguing molecules involved in protein manufacture are the set of 20 molecular machines that fasten amino acids onto transfer RNAs. They are called aminoacyl-tRNA synthetases (aaRS) and it is their job to be certain that the correct amino acid is mated to the correct transfer RNA (tRNA). They are like language interpreters, in that they understand both the DNA language of nucleotides and the protein language of amino acids. Just like an interpreter must carefully match an English word to its Chinese equivalent, the aaRS interpreters are key players for ensuring the resulting protein chain is spelled correctly…. in the cell, mistakes can be disastrous, leading to cell death. One difficulty of their job is that some amino acids are very similar to others. Linus Pauling once predicted an error rate of 1 out of 5 (80% accuracy) between isoleucine and valine, since they are differ only in weak van der Waals forces; but experimental evidence shows that the aaRS interpreter scores correctly 2999 times out of 3000 (99.67% accuracy).

An international team of biochemists publishing in the April 25 issue of Molecular Cell has followed the activity of a couple of these interpreters in unprecedented detail. Before attaching the amino acid, the aaRS machine validates it with a “double-sieve” mechanism, which is like forcing the entrant to open two locks with two independent keys, or making him supply two passwords to two different security guards. It performs both pre- and post-transfer editing. In other words, it validates the incoming amino acid before attachment, and double-checks it after attachment. To begin with, the attachment will not proceed unless the tRNA is charged and the amino acid is activated. The active site for the leucine aaRS machine includes a “discrimination pocket” for the side chain of the amino acid leucine. Simultaneously, it authenticates the adenine of the RNA. If the parts don’t match, or a hacker tries to sneak past, the aaRS machine holds the amino acid in position to be hit by the water-balloon firing squad; an incoming water molecule hydrolyzes both substrates, so that no further harm will come from the mismatched tRNA. The properly-edited tRNA then moves to another machine complex, the ribosome, that joins the amino acids together on an assembly line; here, additional proofreading mechanisms check for accuracy. Then the assembled protein chain moves onto the chaperone for correct folding, then to the intercellular railroad for shipping, etc.
The team found a critical aspartic acid in the active site of the leucine aaRS interpreter that is “universally conserved” in very different organisms. Mutating it to something else, like alanine, destroys the editing function. So far, scientists have learned about four proteins that can deacylate charged tRNAs, and they have “completely different structural frameworks.” Small changes in these machines also cause a “dramatic effect upon editing.” The accuracy of the aaRS system is just one of many levels of quality control ensuring cell survival. The authors state, “Our results demonstrate the economy by which a single active site accommodates two distinct substrates in a proofreading process critical to the fidelity of protein synthesis.”

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Your Body Has Transistors Superior to Intel’s 05/01/2003
Roderick MacKinnon’s team has done it again. The headline at Rockefeller University proclaims, “Voltage-dependent channel structure reveals masterpiece responsible for all nerve, muscle activity.” Building on the art metaphor, the news release begins, “Scientists studying the tiny devices — called voltage-dependent ion channels — that are responsible for all nerve and muscle signals in living organisms for 50 years have been working like a bunch of blindfolded art critics. ... Rockefeller’s Roderick MacKinnon, M.D., a Howard Hughes Medical Institute Investigator, Youxing Jiang, Ph.D., and their colleagues have removed the blindfold to reveal a masterpiece of nature’s engineering” :
The masterpiece is an exquisite voltage-regulated pore in the cell membrane that attracts and transmits potassium ions, maintaining an electrical potential with performance specs superior to man-made transistors. The team found that the channel operates with four charge-sensitive protein paddles around the periphery of the channel. They open to permit the correct ions through, and close to adjust the voltage. Proper voltage is maintained via a feedback loop that is sensitive to changing conditions in the environment. Their experimental results made the cover story of the May 1 issue of Nature.
Potassium channels are vital to muscle and nerve activity, and are highly conserved in all organisms, from the Archaea living around hydrothermal vents at the bottom of the ocean, to the human gymnast on the high bar. The importance of these molecule-size gates is summed up in the news release: “The entire sequence of events takes only a few milliseconds, and occurs tens of thousands of times every day in human beings and organisms of all varieties. Without this hair trigger electrical system, life would be more than calm. There would be scant possibility of thinking, breathing or movement.”

Are Germs Good Bugs Gone Bad? The Case of Anthrax 05/01/2003
Now that the anthrax genome has been decoded, scientists are surprised that most of it looks like another milder bacterium, Bacillus cereus. Only about 3% of their genomes are significantly different. In addition, the pathogenic genes are not in the nucleus, but in plasmids (smaller, circular strands of DNA in the cytoplasm). They give the appearance of having been imported by horizontal gene transfer. One of the papers in Nature suggests that both bacteria acquired toxic elements from soil bacteria in this manner, and “Other major differences between B. anthracis and B. cereus may have been effected through altered gene expression rather than loss or gain of genes.” Some are wondering if anthrax acquired its toxicity recently. One team asks, “Findings from this genome sequence analysis raise further questions about the biology of B. anthracis; for instance, what are the roles of putative ‘virulence’ genes in close relatives of B. anthracis that do not cause anthrax, and do they actually contribute to virulence in B. anthracis?
EurekAlert summarizes two papers in the May 1 issue of Nature that report the decoding of the anthrax genome.

Not All Pseudogenes are Pseudo Genes 05/01/2003
At least one pseudogene has a function, claims a team scientists from Japan and UC San Diego (see UCSD Health Science News). Long assumed to be dead copies of true genes that are devolving into useless relics, pseudogenes, which are common in eukaryotic DNA, may not be so useless after all. The team found a pseudogene that, while not coding for a protein, affects the expression of the true gene. The pseudogene apparently stabilizes the expression of a similar protein-coding gene on another chromosome. Without the pseudogene, lab mice developed abnormal kidneys and bones. The team discovered the function of the pseudogene by accident, reports SciNews, as they were preparing the mice for a different experiment. They suspect similar mechanisms may be at work in most other pseudogenes, and “hope to show that pseudogene-gene interaction is a general mechanism taking place in many cellular interactions.” Their technical paper is published in the May 1 issue of Nature Science Now explains that pseudogenes may help keep normal copies functioning.

Protein Has Its Own Private Dressing Room 05/05/2003
Any star of stage and screen has her own private dressing room, and so does the star of cellular activity, the protein. But the protein’s dressing room would make the actress envious; it has a powered double door.
In the May 2 issue of Cell, a team of Stanford scientists studied the ATP-powered lid on one of these dressing rooms, called chaperonins, or chaperones from their role as supervisors of protein folding. Chaperonins are large, complex proteins shaped somewhat like a barrel with a lid. When a newly-joined chain of amino acids comes off the ribosome assembly line, it is subject to damage from the beehive of activity going on in the cytoplasm. It needs a quiet place to fold. The chaperone lid opens, the polypeptide enters, the lid closes, and safe inside, the chain collapses into its precise shape it needs to function. Then the lid opens and the protein exits, ready to go on-stage.
Any action in the cell needs power. The lid on the chaperone is powered by ATP, the common energy currency in the cell. But ATP alone was not enough; As near as these scientists could tell, the camshaft (gamma subunit) on the ATP synthase motor is what triggers the lid to close. The Stanford team found that prokaryotic chaperones have lids that snap on from the outside, but eukaryotic chaperones have a built-in lid. In either case, the lid closing encapsulates the protein chain inside, and is essential for the chain to complete its folding operation; chaperones without lids could not produce folded proteins. Instead, like an actor getting the hook, a guard named protease takes the misfolded protein to the unemployment desk.
Some proteins, like actin, require the help of this secure room to fold; others fold spontaneously inside. The next turn of the cycle opens the door, and out pops the protein for the production, complete with hook resistance.

Enzyme Speeds Up Slow Reaction by 10exp21 05/06/2003
The slowest known biological reaction would take a trillion years on its own, but an enzyme does it in 10 thousandths of a second. Richard Wolfenden of the University of North Carolina discovered this amazing fact by studying the reaction time of phosphate monoesters that are commonly used in cell signaling. The earlier record he had published in 1998 was 78 million years for an uncatalyzed biological transformation that is “absolutely essential” for creating the building blocks of DNA and RNA. This new record means that you could only expect the reaction to occur once in 100 times the assumed lifetime of the universe without the help of the enzyme. Paraphrasing Wolfenden, “that information would allow biologists to appreciate what natural selection has accomplished over the millennia in the evolution of enzymes as prolific catalysts,” says EurekAlert where this story can be found.

How a Mosquito Became Insecticide Resistant 05/08/2003
A French team publishing in the May 8 issue of Nature studied why disease-carrying mosquitoes became resistant to insecticides. It was due to “a loss of sensitivity of the insect’s acetylcholinesterase enzyme to organophosphates and carbamates” that are ingredients of the pesticides. In some cases a single point mutation conferred the resistance.

Automatic Bandages in 10 Seconds 05/08/2003
The gym class may have a first aid kit with Ace bandages, gauze and adhesive pads, but at the cellular scale, the first aid is automatic. In the May 8 issue of Nature, Juliet A. Ellis from King’s College, London, describes how your body has a fast-acting, automatic bandaging system:

“Cell membranes in tissues such as skin, gut and muscle are routinely exposed to mechanical damage, which can produce holes in them. When that damage is not repaired, the consequences can be severe - often resulting in cell death - and may contribute to the development of the muscle degenerative diseases termed muscular dystrophies. From a combination of observations on human muscular dystrophy patients and experiments with mice, Bansal et al. (page 168 of this issue) now report that a protein called dysferlin is a component of the mechanism for resealing the holes, and thus healing the muscle membrane.
Membrane resealing is generally carried out by a mechanism that resembles the calcium-regulated release of vesicles from a cell (exocytosis). The repair pathway is initiated by an influx of calcium through a wound, resulting in an increase in calcium levels at the site of injury. This, in turn, triggers the accumulation of vesicles, which fuse with one another and then with the plasma membrane, within the injury. A 'patch' is thereby added across the wounded area, resealing the plasma membrane. The entire process - which remains largely mysterious - takes between ten and thirty seconds.”

For this to work, the cell needs several coordinated mechanisms: a way to sense the damage, a way to signal the repair team, the materials available to make the patch, and procedures for applying the patch and closing out the alarm.

Treasure Found in DNA Junkyard 05/23/2003
“Not Junk After All,” says Wojciech Makalowski of so-called “junk DNA” (a term coined by the late Sozumu Ohno to describe apparently useless, repetitive sequences in the genome that do not code for genes). Writing in the May 23 issue of Science, he says the junkyard was really a treasure mine :

Although catchy, the term “junk DNA” for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure.
How do the mislabeled pieces of junk shine like gems? They apparently regulate the expression of gene-coding regions through alternative splicing. Describing an example published by an Israeli team in the same issue of Science, Makalowski explains that the alternative splicing involves an interplay with the giant molecular machine called the spliceosome, and is finely tuned:

"It is even more tricky to maintain the delicate balance of signals that cause an exon to be spliced alternatively--you make one mistake (a point mutation) and either a splicing signal becomes too strong and an exon is spliced constitutively, or the signal becomes too weak and an exon is skipped."

Makalowski thinks the additional copies of genes allow one to be preserved and the other to be a source of evolutionary novelty.

“Unfortunately, most mutations will lead to abnormal proteins and are likely to result in disease. Yet a small number may create an evolutionary novelty, and nature’s “alternative splicing approach” guarantees that such a novelty may be tested while the original protein stays intact.
Another way to exploit an evolutionary novelty without disturbing the function of the original protein is gene duplication (see the figure). Gene duplication is one of the major ways in which organisms can generate new genes. After a gene duplication, one copy maintains its original function whereas the other is free to evolve and can be used for “nature’s experiments.”
He realizes he is sounding anthropomorphic, but sheepishly continues his analogy in the concluding sentences (emphasis added):

"These two papers demonstrate that repetitive elements are not useless junk DNA but rather are important, integral components of eukaryotic genomes. Risking personification of biological processes, we can say that evolution is too wise [sic] to waste this valuable information. Therefore, repetitive DNA should be called not junk DNA but a genomic scrap yard, because it is a reservoir of ready-to-use segments for nature’s evolutionary experiments."

The other paper he refers to was a study by Iwashita et al a few years ago that suggested transposable elements permit a kind of modular programming. A cow was found to have two copies of a gene, but one copy had an inserted endonuclease module. He concluded that this arrangement allowed it to evolve a new function while the other copy without the module maintained the cow’s original fitness.

Factoid: The Nuclear Pore Complex 06/02/2003
Impress your friends today: tell them about Nuclear Pore Complexes. These are elaborate, specialized pores in the nuclear membranes that surround the nucleus of each cell in your body like a skin. The pores look something like complex basketball hoops with rings and studs that act like electronic gates. Their job is to control traffic in and out of the nucleus. Each nuclear pore complex works so fast, it can authenticate somewhere between 520 and 1000 pieces of cargo per second. A typical nucleus has about 2000 to 4000 or more of these gates, which are made up of 30 or more very complex proteins. They all have to be disassembled and reassembled every time a cell divides. (Believe it or not, this is a vastly oversimplified summary of a much more complicated picture.)
Source: Developmental Cell, June 2, 2003, review article by Suntharalingam and Wente.

Germs For Your Health 06/04/2003
“Most people’s views of bacteria are of menacing, disease-producing entities. Au contraire,” says Jeffrey I Gordon of Washington University School of Medicine (St. Louis), quoted in Science News 163:22, p. 344. “I think that most of our encounters with bacteria are mutually beneficial, friendly, and part of our normal biology. .... They’ve insinuated themselves into our biology and coevolved with us.”
The article by John Travis lists several ways our intestinal flora help us. They break down complex sugars, signal the gut lining to stimulate defenses against pathogens, help the gut mature, and help it detoxify compounds. One kind is mostly active during lactation to help an infant digest complex sugars in the mother’s milk – in fact, the Nestle company farms this bacterium and incorporates into some of its infant formula and yogurt “to promote gastrointestinal health.” Scientists have found that rodents raised without a certain bacterium must consume about 30 percent more calories to maintain their body weight; this means the bacterium helps a mammal to digest its food. Other microbes stimulate our own cells to put up an “electric fence” to keep out harmful germs, but are not affected themselves. In return, the friendly bacteria get to feed off leftovers. There may be 1,000 different kinds of bacteria living in our intestines. Scientists have barely begun to explore the variety of these organisms, which according to estimates “may together possess as many unique genes as a person does, and perhaps far more.” Your little passengers “outnumber all the cells in your body, perhaps by as much as a factor of 10.”

How to Tweak a Translator 06/09/2003
As discussed here several times before (April 29, Nov. 1), DNA translation depends on a family of 20 specialized proteins that act as language interpreters. They are called the aminoacyl-tRNA synthetases (aaRS), and their unique property of being able to precisely match an amino acid to the transfer RNA that codes for it means they understand two codes: the nucleotide code of DNA, and the amino-acid code of proteins. How could such an interpreter evolve?
In the June 9 online preprints of the Proceedings of the National Academy of Sciences, three French biochemists claim to have fused parts together to create an “artificial” tRNA synthetase. Each aaRS molecule has four functional parts: a domain that binds AMP to the amino acid, a domain that acylates the amino acid, a domain that edits the tRNA attachment, and a domain that joins the two together. The ability of each of these functions to work depends on the precise order of the amino acids in the synthetase (for alanine’s synthetase, 876 of them). These scientists took out the normal part of amino acids #368-461, the part involved in aminoacylation, and fused in some of their own polypeptides they had selected for their ability to acylate the amino acid alanine. Out of seven mutants, some did better than others, and none showed any significant energy penalty in the other end’s ability to bind RNA.
They also tried substituting other amino acids in the active site of their “artificial” synthetase. Each substitution reduced the ability to acylate alanine, some 2-fold, some 5-fold and with three changes, 10-fold. Each mutant also lost ability to act specifically on alanine. There did not seem to be much tolerance, therefore, for changes in a 10-peptide sequence located in the heart of the active site.
What do they make of this? In the discussion, they feel they have demonstrated that fusing a replacement string into part of the synthetase did not destroy its ability to do its other functions. “Importantly,” they say,

“the two components, adenylate synthesis and specific RNA binding, were generated independently. ... Thus, the results are consistent with the idea that early tRNA synthetases arose from small, idiosyncratic RNA-binding elements being fused to domains for adenylate synthesis. These RNA-binding elements might have developed originally to bind and protect ribozymes (to give early ribonucleopeptides or ribonucleoproteins; refs 44-47). The fusions of RNA-binding peptides to domains for adenylate synthesis may have been the first step in developing protein-based synthetases that overcame the ribozyme-based system of aminoacylation.”

Since the cost to the RNA-binding portion was inconsequential, they feel the two main functions of the synthetase could have arisen independently, and serendipitously come together to take over the job ribozymes were doing [i.e., in the hypothetical RNA World scenario].

Picture of Protein Evolution Emerging? 06/16/2003
“Most proteins have been formed by gene duplication, recombination, and divergence,” declare scientists from Cambridge and Stanford in the June 13 issue of Science. “Proteins of known structure can be matched to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins of these processes.” With growing numbers of genomes decoded, they feel we are well on the way to answering fundamental questions about how the huge assortment of proteins arose:

“During the course of evolution, forms of life with increasing complexity have arisen. What are the mechanisms that have produced the increases in protein repertoires that underlie the evolution of more complex forms of life? How are proteins organized to form pathways? Answers to such questions at the molecular level began to appear 40 years ago, but it is only with the advent of complete genome sequences that we have begun to get a comprehensive view.”

“At present,” they admit, only “close to 50% of the sequences in the currently known genomes are homologous to proteins of known structure,” yet “this half of the protein repertoire have given us a detailed picture of its evolution.” They discuss how proteins fall into domains, and these are organized into families that seem to obey a power-law distribution; i.e, “A few families have many members and many families have a few members.” Even proteins with different sequences can often be matched with others possessing similar structure. Many of these are paired with other domains. Of all the million-plus possible pairs of known families, only a few thousand are used. This, they feel, is evidence of selection for function. Also, the fact that “combinations of particular pairs of domains are found in only one sequential order ... suggests that conservation of sequential order in domain combinations is usually found because the combinations descend from a common ancestor.”
The authors feel confident that we understand the basics of how new complexity arises from the protein pool:

“It is now clear that the dominant mechanisms that produce increases in protein repertoires are (i) duplication of sequences that code for one or more domains; (ii) divergence of the duplicated sequences by mutations, deletions, and insertions to produce modified structures that may have useful new properties and be selected; and, in some cases, (iii) recombination of genes that results in novel arrangements of domains.”

But how would metabolic pathways arise? They introduce the problem: “Proteins do not function by themselves but as part of an intricate network of physical complexes and pathways. How does the duplication, divergence, and recombination process fit into the formation or extension of pathways?” They propose that mutated proteins might either be recruited to new substrates within existing pathways, or jump to different pathways. They observe, “An examination of the functions of the members of different families of domains shows that, nearly always, it is the catalytic mechanism or cofactor-binding properties that are conserved or slightly modified and the substrate specificity that is changed. This suggests that it is much easier to evolve new binding sites than new catalytic mechanisms.” This tends to scramble the evolutionary picture, though: “This has led to a mosaic pattern of protein families with little or no coherence in the evolutionary relationships in different parts of the network.” Can the evolutionary history be seen by comparing unrelated organisms, then?

“The comparison of enzymes in the same pathway in different organisms also shows that proteins responsible for the particular functions can belong to unrelated protein families. This phenomenon is called “nonorthologous displacement”. Variations come not just from changes in specific enzymes. In some organisms, sections of the standard pathway are not found and the gaps are bypassed through the use of alternative pathways. Together, these variations produce widespread plasticity in the pathways that are found in different organisms....

One final question remains: how did the first proteins originate? And are new ones originating now?

“The earliest evolution of the protein repertoire must have involved the ab initio [Lat., from the beginning] invention of new proteins. At a very low level, this may still take place. But it is clear that the dominant mechanisms for expansion of the protein repertoire, in biology as we now know it, are gene duplication, divergence, and recombination. Why have these mechanisms replaced ab initio invention? Two plausible causes, which complement each other, can be put forward. First, once a set of domains whose functions are varied enough to support a basic form of life had been created, it was much faster to produce new proteins with different functions by duplication, divergence, and recombination. Second, once the error-correction procedures now present in DNA replication and protein synthesis were developed, they made the ab initio invention of proteins a process that is too difficult to be useful.”

In conclusion, they remind the reader that genome size is not the measure of complexity (rice has more genes than people); instead, “complexity does seem to be related to expansions in particular families that underlie the more complex forms of life.” So the key to understanding the evolution of the protein repertoire will be to compare how families of proteins in diverse organisms have been duplicated and recombined.

Bacteria More Orderly Than Previously Known 06/17/2003
Bacteria are not simple bags of protoplasm. Since they lack the organelles and nuclei that eukaryotic cells possess, scientists used to think their contents were fairly unstructured and homogeneous. That view is changing, say Zemer Gitai and Lucy Shapiro in the June 16 online preprints of the Proceedings of the National Academy of Sciences. “Historically,” they agree, “perhaps because of their general lack of compartmentalized organelles, bacteria were viewed as relatively uniform at the subcellular level.” New microscopic techniques are unveiling highly ordered structures, like protein spirals and rings that oscillate between the poles and allow the cell to locate the midpoint for cell division. “Perhaps the most important lesson to be learned from the work by Shih et al,” (who imaged the spiral proteins) “is that the more closely we look, the more order we see within bacterial cells. The fact that the phrase ‘bacteria are not just small bags of enzymes’ has become cliché is a sign that bacterial cell biology is coming of age.”

For a related story, see our Jan 16 headline about spiral action of the bacterial cytoskeleton that repairs the inner cell wall.

Surprise: Y Chromosome Protects Itself with Palindromes 06/18/2003
Cheer up, men: your Y chromosome is not going extinct. Since the Y has no backup copy, geneticists thought it might mutate itself into useless junk in just 10 million years. Well, the Y chromosome map has just been completed, reports Nature Science Update, and of all the clever things, the Y has built-in self-defense in the form of palindromes. Just like the phrase “Madam, I’m Adam” can be read the same backwards and forwards, there are large gene-coding regions on the Y that can be decoded in either direction. The article explains:

“These palindromes house many genes - which means that there is a copy at each end of the palindromic sequence. These provide back-ups should harmful mutations arise. The mirror-image structure also allows the arms to swap position when DNA divides. Genes are shuffled and bad copies are purged.”

David Page at MIT remarked, “The Y chromosome is a hall of mirrors.” More surprises are expected now that the full map of the chromosome has been published (it’s the cover story of Nature June 19). Now that the male chromosome “reveals that we have underestimated its powers of self-preservation,” maybe men will finally start getting some respect.
“Male chromosome full of surprises,” is the way Science Now entitled their summary of the findings. The Y is not a graveyard of genes, nor a shriveled up remnant of the larger X chromosome. Its new-found capabilities, dynamically shuffling its genes to weed out defects, has given scientists a new appreciation for it. As one researcher put it, this has “brought a lot of honor to males.”

Scientists Watch Motors Unwind DNA 06/19/2003
Andrew Taylor and Gerald Smith from Fred Hutchinson Cancer Research Center (Seattle, WA) announced in Nature June 19 that “RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity.” In the same issue, Mark S. Dillingham, Maria Spies and Stephen C. Kowalczykowski of U.C. Davis came to a similar conclusion. Working independently, these teams watched an important molecular motor in action and determined that it is two motors in one, with a slow motor and fast motor working side by side on the same track. How can that be, and why?
RecBCD helicase is the molecular machine that travels along a DNA double helix, unwinds it, and separates the strands so that the translation machinery can get to it. This combination enzyme (RecB + RecC + RecD) is a member of a superfamily of helicases, or enzymes able to unwind and separate DNA. Simpler helicases separate the two DNA strands into a Y-like tail, but RecBCD has the unusual property of creating a loose tail on the RecD side and a loop and a short tail on the RecB side (RecC, not a motor, appears to help RecB in its action). Combined, RecBCD is among the fastest of helicases: it can cover 370 base pairs per second, according to Taylor and Smith, or up to 1000 base pairs per second, according to Kowalczykowski et al.
Both the RecB and RecD motors can travel along DNA separately, but are polar opposites: one moves along one strand, one along the other. Of the two, RecD is the speed demon; RecBC only moves 20% as fast. The motors are not nearly as fast or stable acting alone. Separately, they fall off the track after 50 base pairs, but together, can cover 400-600 times as much ground: 20,000 (Taylor and Smith) or 30,000 (Kowalczykowski) at full speed.
So why two engines in this race car? Taylor and Smith suggest that it adds stability; a motor is less likely to fall off the DNA track when combined with another, but why the speed difference? This will take more study. All they can conclude is, “This asymmetric feature might impart RecBCD enzyme’s asymmetry in other aspects of its promotion of genetic recombination.”

Cell to Phagocyte: I’m Dying – Eat Me 06/27/2003
Cells go the way of all the earth, but their society cleans up after them. This occurs through an elaborate signalling procedure that biochemists are beginning to uncover, as explained in a Minireview in Cell, June 27 by Kodi S Ravichandran (Univ. of Virginia). A cell undergoing death throes by caspase activation (in itself an elaborate shutdown process) sends out “eat me” signals that are recognized by the roving clean-up squad, the phagocytes. Normally, a cell wears a “Don’t eat me” tag, but this is removed and a phosphatidylserine (PS) tag pops up on the outer membrane. Simultaneously, LPC and/or other signals are secreted in search of a nearby phagocyte, with a “silent invitation to dinner.” The dying cell wears the Eat-Me signals on its outer membrane. An approaching phagocyte turns on anti-inflammation signals, as if to say to others nearby, “Nothing to get inflamed about; I can handle this one.” After engulfing the dying cell, it re-arms the inflammation alarm.
Through this system, needless inflammation is avoided, and the streets and alleys are kept clear of cellular corpses. The author summarize, “An evolutionarily conserved machinery exists for engulfment of apoptotic cells from worm to mammals.”

Last edited by bob b; October 22nd, 2006 at 10:07 AM.

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

Horizontal Gene Transfer More Widespread than Thought 07/10/2003
A study of plant mitochondrial genomes published in the July 10 issue of Nature found five cases of horizontal gene transfer (HGT) between distantly related plants. This was unexpected, since HGT was thought to be only significant among bacteria and virtually absent from eukaryotes. They feel these discoveries are only the “tip of a large iceberg” that may cause major rethinking of the role of HGT not only in plants and mitochondrial DNA, but also in animals and in nuclear DNA. “Our findings raise many other questions,” say the authors, Bergthorsson, Adams, Thomason and Palmer, in “Widespread horizontal transfer of mitochondrial genes in flowering plants.”

Bacterial Flagellum Rotation Speed Depends on Proton Flow 07/11/2003
A bacterial motor responds to the fuel available. Howard Berg of Harvard, one of the world’s authorities on the bacterial flagellum, has established that there is a linear relation between proton motive force (pmf) and rotation speed. In a paper in the Proceedings of the National Academy of Sciences (July 11 online preprints), he says this was known for high speeds, but his present work establishes it for low speeds also.
To measure these things, Berg took an E. coli bacterium with two flagella, and attached one to a small latex bead, and the other to a rigid surface. The first one could turn easily, but the other had a heavier load – the whole body of the bacterium. Plotting all the numbers, he found a linear relationship between pmf and rotation rate, from stalling speed up to 380 Hz at zero load. “The present work shows that a linear relation is true more generally,” he said, “providing an additional constraint on possible motor mechanisms.” He admitted in the discussion section that, “It is not yet known how the motor generates torque.”

Simplest Protein a “Paradigm of Complexity” 07/15/2003
Myoglobin (Mb), the substance that gives muscles their red color, was one of the first proteins studied. “Thirty years ago, ” state Frauenfelder, McMahon and Fenimore in a Commentary in the July 14 Proceedings of the National Academy of Sciences, “the textbook function of Mb, storage of dioxygen at the heme iron, was considered to be simple, fully understood, and consequently boring. Since then, the situation has changed: Mb is no longer fully understood.” Scientists are finding out that this single-chain (monomeric) protein, folded into an apparently shapeless blob, has multiple functions – and these derive from its ability to dynamically change shape:
A protein does not exist in a unique conformation but can assume a very large number of somewhat different conformations or conformational substates. ... If a protein had just a single conformation, it could not function and would be dead like a stone.
Proteins react to their environment, the pressure and temperature, and also to the atoms in their vicinity. In the case of myoglobin, oxygen and carbon monoxide molecules are able to cause it to open up, “as if the drawbridges ... were controlled from the outside of the castle!” they state with evident surprise. They conclude that this best-studied protein still sports some fundamental problems for biochemists and biophysicists to solve. What we are learning about its conformational motions during function makes it no longer boring! It symbolizes the beginning of discoveries that will undoubtedly be valid for all proteins. The authors call myoglobin the “hydrogen atom of biology,” analogous to the detailed model Bohr made of the simplest of atoms when he attempted to begin to understand the basic laws governing all atoms. As such, “The large number of substates and their organization and importance for function make Mb a paradigm of complexity.”

Cell Translation Uses Rotating Locks and Keys 07/21/2003
A French team has studied one of the molecules involved in the translation of DNA to protein, and found that it does some nifty shape changes when its accessory proteins are in place. The molecule is threonyl-tRNA synthetase, one of the family of 20 specialized molecules that attach the appropriate amino acid to its matching transfer-RNA (tRNA) carrier. The operation involves four parts: the synthetase, the tRNA, the amino acid threonine, and ATP. The abstract describes some of the activity observed:

“The tRNA, by inserting its acceptor arm between the N-terminal domain and the catalytic domain, causes a large rotation of the former. Within the catalytic domain, four regions surrounding the active site display significant conformational changes upon binding of the different substrates. The binding of threonine induces the movement of as much as 50 consecutive amino acid residues. The binding of ATP triggers a displacement, as large as 8 angstroms at some C positions, of a strand-loop-strand region of the core beta-sheet. Two other regions move in a cooperative way upon binding of threonine or ATP: the motif 2 loop, which plays an essential role in the first step of the aminoacylation reaction, and the ordering loop, which closes on the active site cavity when the substrates are in place. The tRNA interacts with all four mobile regions, several residues initially bound to threonine or ATP switching to a position in which they can contact the tRNA. Three such conformational switches could be identified, each of them in a different mobile region. The structural analysis suggests that, while the small substrates can bind in any order, they must be in place before productive tRNA binding can occur.”

The paper by Moras et al. is published in the upcoming Journal of Molecular Biology, August 2003. (For a previous headline on the tRNA synthetase family, see June 9.)

DNA End Capping More Complex Than Thought 07/25/2003
An idea has been floating around for years to explain why cells grow old and die. Biochemists have known that DNA strands have end caps, called telomeres. These caps keep them from unwinding or sticking to other DNA strands, which, when it occurs, creates a crisis in the cell, and usually triggers cell death or apoptosis. Each time a cell divides, the story goes, it loses a telomere, because the duplication machinery could not get a grip on the last cap. This seemed to act like a countdown timer. When the telomeres hit zero, pop goes the apoptosis. An enzyme has been known, however, that repairs telomeres. Named telomerase, it was thought to work only in certain kinds of cells, and has been implicated in cancer. The idea was that out-of-control telomerase made cancer cells immortal when they should have died.
Well, once again, the picture is more complicated than that. An international team has just reported in the journal Cell 07/25/2003 that “Telomerase Maintains Telomere Structure in Normal Human Cells.” They found that all cells express this repair enzyme, and that there is a complicated interplay between regulatory factors to keep a normal cell functioning through multiple cell divisions, with just the right number of telomeres for its needs and environment. Their observations “support the view that telomerase and telomere structure are dynamically regulated in normal human cells,” and that telomere length alone is not a sign of old age and impending death.
Only when things go wrong with these regulatory mechanisms do cells either lose their last telomeres and die, or go wild into immortal replication cycles as in cancer. Telomerase is a key ingredient both in the regulation of cell proliferation and replicative lifespan, they found. Targeting telomerase in cancer treatment as a bad molecule may not be wise, therefore. It’s apparently a vital part of a normal cell’s operation. One thing is clear: “the relationships among telomere length, telomere expression, and replicative lifespan are more complex than previously believed.”

Gates of the Membrane 08/06/2003
A couple of papers in last week’s issue of Science reveal details of just two of nearly 360 specialized proteins in cell membranes that ferry necessary molecules across “the otherwise impermeable barrier imposed by the phospholipid bilayer.” They look like clever rockers forming a funnel on one side of the membrane. When the right molecule falls in, the funnel inverts and ejects the molecule onto the other side. These act as “molecular pumps, translocating their substrates across membranes against a concentration gradient; this thermodynamically unfavorable process is powered by coupling to a second, energetically favorable process such as ATP hydrolysis or the movement of a second solute down a transmembrane concentration gradient.” The two studied here, LacY and GlpT, use the latter method.

Nanocells are Naah, No Cells 08/09/2003
Earlier claims that nanobacteria exist, tiny cells an order of magnitude smaller than the smallest known cells, are apparently unfounded. Nature Science Update reports on a paper in Geology Aug. 2003 that the alleged fossils of nanobacteria appear to be by-products of enzyme-driven tissue decay; i.e., just clumps of leftover digested material from larger living things.

Beautiful: The Maximum Output from Minimal Cells 08/13/2003
Dry science journals do not often talk about beauty, but Donald A. Bryant (Penn State) entitled his Commentary in the Proceedings of the National Academy of Sciences (online preprints, 08/13/03), “The beauty in small things revealed.” There is a tiny, minimalist cyanobacterium in the oceans that is so plentiful in numbers, it and one other species might account for as much as two-thirds the total CO2 fixation in the oceans, and one-third the primary biomass production on earth. This makes it a key player in the global carbon cycle. “The contribution of marine photosynthesis to the global carbon cycle was grossly underestimated until recently,” Bryant comments. “...As every microbiologist inherently knows, little things can be the cause of much greater things that are often of utmost importance, and this is especially true of phytoplankton.” Yet this key player was only discovered 15 years ago.
Bryant refers to another paper in the same issue of PNAS by Dufresne et al., who sequenced the genome of this organism named Prochlorococcus marinus. They found it to be very near the theoretical lower limit in size for an autotrophic (self-feeding) photosynthetic organism, one ten-millionth of a cubic meter. “Because of its remarkable compactness,” they write, “the genome of P. marinus SS120 might approximate the minimal gene complement of a photosynthetic organism.” Some of its systems – DNA repair, chaperones, transport systems, motility, and nitrogen metabolism among them – are scaled down from other, larger bacterial cells. It also lacks duplicate genes for photosystem II components (although it has the complete set). But it has enough genetic information and synthetic machinery to make all its own nutrients with sunlight. This is a non-trivial toolkit: “it must have the ability to synthesize all cellular constituents, including amino acids, nucleotides, coenzymes, etc. from CO2 and mineral salts.” The small size of Prochlorococcus also has the advantage of a greater surface-to-volume ratio, less self-shading, and more efficient light capture. “Being minimalistic,” Bryant says, “does not necessarily mean that Prochlorococcus sp. is less competitive.” The little cells can diversify and adapt well. “Yes,” he concludes, “small things can be simple and yet highly successful on a global scale.” There is a lay summary of the article on Nature Science Update by John Whitfield.

Understanding Cells: Think Information, Logic Circuits 08/21/2003
The Concepts article in Nature 08/21/2003 is about “Systems biology: Understanding Cells” by Paul Nurse. A striking feature of his article is the repeated use of the word information:

“Many of the properties that characterize living organisms are also exhibited by individual cells. These include communication, homeostasis, spatial and temporal organization, reproduction, and adaptation to external stimuli. Biological explanations of these complex phenomena are often based on the logical and informational processes that underpin the mechanisms involved....
Most experimental investigations of cells, however, do not readily yield such explanations, because they usually put greater emphasis on molecular and biochemical descriptions of phenomena. To explain logical and informational processes on a cellular level, therefore, we need to devise new ways to obtain and analyse data, particularly those generated by genomic and post-genomic studies.
An important part of the search for such explanations is the identification, characterization and classification of the logical and informational modules that operate in cells. For example, the types of modules that may be involved in the dynamics of intracellular communication include feedback loops, switches, timers, oscillators and amplifiers. Many of these could be similar in formal structure to those already studied in the development of machine theory, computing and electronic circuitry.”

Nurse identifies three types of information seen in cells: sequence data, interaction data, and functional data. He feels that this logical, informational approach to the study of cells will be more productive than just studying the individual molecules in detail:

“A useful analogy of what is being proposed is the analysis of an electronic circuit. Once the detailed operations of different types of electronic components have been identified, it is possible to gain insight into what an electronic circuit can do simply by knowing what components are present and how they are connected, even if their precise dynamic behaviour has not been determined. The various logical and informational modules implicated in a biological phenomenon of interest have to be integrated in order to generate a better understanding of how cells work.”

Paul Nurse feels that this information-theoretic approach to the cell could generate a great deal of experimental work. “The identification and characterization of these modules will require extensive experimental investigation, followed by realistic modelling of the processes involved,” he predicts. “Such analyses would allow a catalogue of the module types that operate in cells to be assembled.” But this approach will work only if there is a finite set of such modules:

“The success of this general approach depends on there being a limited set of biochemical activities and molecular interactions that together can solve the myriad logical and informational problems found in biological systems. If there is only a restricted set of processes that are efficient and stable in operation and which have been exploited by evolution [sic], then there should be only a limited set of possible solutions to real biological problems. Of course, if nature shows no such restraint [sic], then we must go back to the drawing-board if we are ever to understand its complexity.”

Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.